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19 \title{UNRES - A PROGRAM FOR COARSE-GRAINED SIMULATIONS OF PROTEINS}
21 \author{Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
24 Scheraga Group\\ Baker Laboratory of Chemistry \\
25 and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1301, USA}
37 %3. General information
39 % 3.2. Functions of the program
40 % 3.3. Companion programs
41 % 3.4. Programming language
44 %5. Customizing your batch and C-shell script
45 %6. Command line and files
48 % 8.1. Main input data file
50 % 8.1.2. Control data (data list format; READ_CONTROL subroutine)
51 % 8.1.2.1 Keywords to chose calculation type
52 % 8.1.2.2 Specification of protein and structure output in non-MD applications
53 % 8.1.2.3. Miscellaneous
54 % 8.1.3. Minimizer options (data list, subroutine READ_MINIM)
55 % 8.1.4. CSA control parameters
56 % 8.1.5. MCM data (data list, subroutine MCMREAD)
57 % 8.1.6. MD data (subroutine READ_MDPAR)
58 % 8.1.7. REMD/MREMD data (subroutine READ_REMDPAR)
59 % 8.1.8. Energy-term weights (data list; subroutine MOLREAD)
60 % 8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
61 % 8.1.10. Amino-acid sequence (free and text format)
62 % 8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
63 % 8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
64 % 8.1.13. Distance restraints (subroutine READ_DIST_CONSTR)
65 % 8.1.14. Internal coordinates of the reference structure (free format; subroutine READ_ANGLES)
66 % 8.1.15. Internal coordinates of the initial conformation (free format; subroutine READ_ANGLES)
67 % 8.1.15.1. File name with internal coordinates of the conformations to be processed
68 % 8.1.16 Control data for energy map construction (data lists; subroutine MAP_READ)
69 % 8.2. Input coordinate files
70 % 8.3. Other input files
72 % 9.1. Coordinate files
73 % 9.1.1. The internal coordinate (INT) files
74 % 9.1.2. The plain Cartesian coordinate (X) files
75 % 9.1.3. The compressed Cartesian coordinate (CX) files
76 % 9.1.4. The Brookhaven Protein Data Bank format (PDB) files
77 % 9.1.5. The SYBYLL (MOL2) files
78 % 9.2. The summary (STAT) file
80 % 9.2.2. MD and MREMD runs
81 % 9.3. CSA-specific output files
82 %10. Technical support contact information
87 \section{LICENSE TERMS}
93 This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
96 This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
99 Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
108 The current and former developers of UNRES are listed in this section in alphabetic
109 order together with their current or former affiliations.
112 Maurizio Chinchio (formerly Cornell Univ., USA)
113 Cezary Czaplewski (Univ. of Gdansk, Poland)
114 Carlo Guardiani (Georgia State Univ., USA)
115 Yi He (Cornell Univ., USA)
116 Justyna Iwaszkiewicz (Swiss Institute of Bioinformatics, Switzerland)
117 Dawid Jagiela (Univ. of Gdansk, Poland)
118 Stanislaw Jaworski (deceased)
119 Sebastian Kalinowski (Univ. of Gdansk, Poland)
120 Urszula Kozlowska (deceased)
121 Pawel Krupa (Univ. of Gdansk, Poland)
122 Rajmund Kazmierkiewicz (Univ. of Gdansk, Poland)
123 Jooyoung Lee (Korea Institute for Advanced Studies, Korea)
124 Adam Liwo (Univ. of Gdansk, Poland)
125 Mariusz Makowski (Univ. of Gdansk, Poland)
126 Magdalena Mozolewska (Univ. of Gdansk, Poland)
127 Marian Nanias (formerly Cornell Univ., USA)
128 Stanislaw Oldziej (Univ. of Gdansk, Poland)
129 Jaroslaw Pillardy (Cornell Univ., USA)
130 Shelly Rackovsky (Mout Sinai School of Medicine, USA)
131 Daniel Ripoll (formerly Cornell Univ., USA)
132 Jeff Saunders (Schrodinger Inc., USA)
133 Harold A. Scheraga (Cornell Univ., USA)
134 Hujun Shen (Dalian Institute of Chemical Physics, P.R. China)
135 Adam Sieradzan (Univ. of Gdansk, Poland)
136 Ryszard Wawak (formerly Cornell Univ., USA)
137 Tomasz Wirecki (Univ. of Gdansk, Poland)
138 Marta Wisniewska (Univ. of Gdansk, Poland)
139 Yanping Yin (Cornell Univ., USA)
140 Bartlomiej Zaborowski (Univ. of Gdansk, Poland)
145 \section{GENERAL INFORMATION}
149 \label{sect:geninfo:purpose}
151 Run coarse-grained calculations of polypeptide chains with the UNRES force field.
152 There are two versions of the package which should be kept separate because of
153 non-overlapping functions: version which runs global optimization (Conformational
154 Space Annealing, CSA) and version that runs coarse-grained molecular dynamics and
155 its extension. Because the installation, input file preparation and running CSA
156 and MD versions are similar, a common manual is provided. Items specific
157 for the CSA and MD version are marked ``CSA'' and ``MD'', respectively.
159 MD version can be used to run multiple-chain proteins (however, that version of
160 the code is a new release and might fail if yet un-checked functions are used).
161 The multi-chain CSA version for this purpose is another package (written largely in
164 \subsection{Functions of the program}
165 \label{sect:geninfo:functions}
170 Perform energy evaluation of a single or multiple conformations (serial and parallel) (CSA and MD).
173 Run canonical mesoscopic molecular dynamics (serial and parallel) (MD).
176 Run replica exchange (REMD) and multiplexing replica exchange (MREMD) dynamics (parallel only) (MD).
179 Run multicanonical molecular dynamics (parallel only) (MD).
182 Run energy minimization (serial and parallel) (CSA and MD).
185 Run conformational space annealing (CSA search) (parallel only) (CSA).
188 Run Monte Carlo plus Minimization (MCM) (parallel only) (CSA).
191 Run conformational family Monte Carlo (CFMC) calculations (CSA).
194 Thread the sequence against a database from the PDB and minimize energy of each structure (CSA).
198 Energy and force evaluation is parallelized in MD version.
201 \subsection{Companion programs}
202 \label{sect:geninfo:companion}
204 The structures produced by UNRES can be used as inputs to the following programs provided
205 with this package or separately:
209 \item{xdrf2pdb} -- converts the compressed coordinate files from MD (but not MREMD)runs into
212 \item{xdrf2pdb-m} -- same for MREMD runs (multiple trajectory capacity).
214 \item{xdrf2x} -- converts the plain Cartesian coordinate files into PDB format.
216 \item{WHAM} -- processes the coordinate files from MREMD runs and computes temperature profiles
217 of ensemble averages and computes the probabilities of conformations at selected
218 temperatures; also prepares data for CLUSTER and ZSCORE.
220 \item{CLUSTER} -- does the cluster analysis of the conformations; for MREMD runs takes the
221 coordinate files from WHAM which contain information to compute probabilities
222 of conformations at any temperature.
224 \item{PHOENIX} -- conversion of UNRES conformations to all-atom conformations.
226 \item{ZSCORE} -- force field optimization (for developers).
230 Please consult the manuals of the corresponding packages for details. Note that not
231 all of these packages are released yet; they will be released depending on their
232 readiness for distribution. Contact Adam Liwo, Cezary Czaplewski or Stanislaw Oldziej
233 for developmental versions of these programs.
235 \subsection{Programming language}
236 \label{sect:geninfo:language}
238 This version of UNRES is written almost exclusively in Fortran 77; some subroutines
239 for data management are in ansi-C. The package was parallelized with MPI.
243 \subsection{References}
244 \label{sect:geninfo:references}
246 Citing the following references in your work that makes use of UNRES is gratefully
250 \renewcommand{\section}[2]{}%
251 \begin{thebibliography}{10}
254 A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, H.A. Scheraga.
255 A united-residue force field for off-lattice protein-structure simulations.
256 I: Functional forms and parameters of long-range side-chain interaction potentials
257 from protein crystal data. {\it J. Comput. Chem.}, {\bf 1997}, 18, 849-873.
259 \bibitem{liwo_1997_02}
260 A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, H.A. Scheraga.
261 A united-residue force field for off-lattice protein-structure simulations.
262 II: Parameterization of local interactions and determination
263 of the weights of energy terms by Z-score optimization.
264 {\it J. Comput. Chem.}, {\bf 1997}, 18, 874-887.
266 \bibitem{liwo_1997_03}
267 A. Liwo, S. O{\l}dziej, R. Ka\'zmierkiewicz, M. Groth, C. Czaplewski.
268 Design of a knowledge-based force field for off-lattice simulations of protein
270 {\it Acta Biochim. Pol.}, {\bf 1997}, 44, 527-548.
274 A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Oldziej, R.J. Wawak,
275 S. Rackovsky, M.R. Pincus, H.A. Scheraga.
276 United-residue force field for off-lattice protein-structure simulations.
277 III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
278 {\it J. Comput. Chem.}, {\bf 1998}, 19, 259-276.
281 A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
282 Cumulant-based expressions for the multibody terms for the correlation between
283 local and electrostatic interactions in the united-residue force field.
284 {\it J. Chem. Phys.}, {\bf 2001}, 115, 2323-2347.
287 J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, H.A. Scheraga,
288 Optimization of parameters in macromolecular potential energy functions by
289 conformational space annealing. {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7291-7298
291 \bibitem{pillardy_2001}
292 J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll,
293 P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga,
294 Development of physics-based energy functions that predict medium-resolution
295 structures for proteins of the $\alpha, \beta$, and $\alpha/\beta$ structural classes.
296 {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7299-7311
299 A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H.A. Scheraga.
300 A method for optimizing potential-energy functions by a hierarchical design
301 of the potential-energy landscape: Application to the UNRES force field.
302 {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2002}, 99, 1937-1942.
304 \bibitem{saunders_2003}
305 J. A. Saunders and H.A. Scheraga.
306 Ab initio structure prediction of two $\alpha$-helical oligomers
307 with a multiple-chain united-residue force field and global search.
308 {\it Biopolymers}, {\bf 2003}, 68, 300-317.
310 \bibitem{saunders_2003_02}
311 J.A. Saunders and H.A. Scheraga.
312 Challenges in structure prediction of oligomeric proteins at the united-residue
313 level: searching the multiple-chain energy landscape with CSA and CFMC procedures.
314 {\it Biopolymers}, {\bf 2003}, 68, 318-332.
316 \bibitem{oldziej_2003}
317 S. Oldziej, U. Kozlowska, A. Liwo, H.A. Scheraga.
318 Determination of the potentials of mean force for rotation about C$^\alpha$-C$^\alpha$
319 virtual bonds in polypeptides from the ab initio energy surfaces of terminally
320 blocked glycine, alanine, and proline. {\it J. Phys. Chem. A}, {\bf 2003}, 107, 8035-8046.
323 A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga.
324 Parameterization of backbone-electrostatic and multibody contributions
325 to the UNRES force field for protein-structure prediction from ab initio
326 energy surfaces of model systems. {\it J. Phys. A}, {\bf 2004}, 108, 9421-9438.
328 \bibitem{oldziej_2004}
329 S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
330 Optimization of the UNRES force field by hierarchical design of the
331 potential-energy landscape. 2. Off-lattice tests of the method with single
332 proteins. {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16934-16949.
334 \bibitem{oldziej_2004_02}
335 S. Oldziej, J. Lagiewka, A. Liwo, C. Czaplewski, M. Chinchio,
336 M. Nanias, H.A. Scheraga.
337 Optimization of the UNRES force field by hierarchical design of the
338 potential-energy landscape. 3. Use of many proteins in optimization.
339 {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16950-16959.
341 \bibitem{oldziej_2004_03}
342 M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, H.A. Scheraga.
343 Molecular dynamics with the united-residue model of polypeptide chains.
344 I. Lagrange equations of motion and tests of numerical stability in the
345 microcanonical mode, {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13785-13797.
347 \bibitem{khalili_2005}
348 M. Khalili, A. Liwo, A. Jagielska, H.A. Scheraga.
349 Molecular dynamics with the united-residue model of polypeptide chains.
350 II. Langevin and Berendsen-bath dynamics and tests on model $\alpha$-helical
351 systems. {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13798-13810.
353 \bibitem{khalili_2005_02}
354 A. Liwo, M. Khalili, H.A. Scheraga.
355 Ab initio simulations of protein-folding pathways by molecular dynamics with
356 the united-residue model of polypeptide chains.
357 {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2005}, 102, 2362-2367.
359 \bibitem{rakowski_2006}
360 F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga.
361 Implementation of a symplectic multiple-time-step molecular dynamics algorithm,
362 based on the united-residue mesoscopic potential energy function.
363 {\it J. Chem. Phys.}, {\bf 2006}, 125, 204107.
365 \bibitem{nanias_2006}
366 M. Nanias, C. Czaplewski, H.A. Scheraga.
367 Replica exchange and multicanonical algorithms with the coarse-grained
368 united-residue (UNRES) force field.
369 {\it J. Chem. Theory and Comput.}, {\bf 2006}, 2, 513-528.
372 A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik, H.A. Scheraga.
373 Modification and optimization of the united-residue (UNRES) potential energy
374 function for canonical simulations. I. Temperature dependence of the effective
375 energy function and tests of the optimization method with single training
377 {\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
379 \bibitem{kozlowska_2007}
380 U. Kozlowska, A. Liwo, H.A. Scheraga.
381 Determination of virtual-bond-angle potentials of mean force for coarse-grained
382 simulations of protein structure and folding from ab initio energy surfaces of
383 terminally-blocked glycine, alanine, and proline.
384 {\it J. Phys.: Condens. Matter}, {\bf 2007}, 19, 285203.
386 \bibitem{chichio_2007}
387 M. Chinchio, C. Czaplewski, A. Liwo, S. Oldziej, H.A. Scheraga.
388 Dynamic formation and breaking of disulfide bonds in molecular dynamics
389 simulations with the UNRES force field.
390 {\it J. Chem. Theory Comput.}, {\bf 2007}, 3, 1236-1248.
393 A.V. Rojas, A. Liwo, H.A. Scheraga.
394 Molecular dynamics with the united-residue force field: Ab Initio folding
395 simulations of multichain proteins.
396 {\it J. Phys. Chem. B}, {\bf 2007}, 111, 293-309.
399 A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz,
400 M. Makowski, R.K. Murarka, H.A. Scheraga.
401 Simulation of protein structure and dynamics with the coarse-grained UNRES
402 force field. In: Coarse-Graining of Condensed Phase and Biomolecular
403 Systems., ed. G. Voth, Taylor \& Francis, 2008, Chapter 8, pp. 107-122.
405 \bibitem{czaplewski_2009}
406 C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga.
407 Application of multiplexed replica exchange molecular dynamics
408 to the UNRES force field: tests with $\alpha$ and $\alpha+\beta$ proteins.
409 {\it J. Chem. Theory Comput.}, {\bf 2009}, 5, 627-640.
412 Y. He, Y. Xiao, A. Liwo, H.A. Scheraga.
413 Exploring the parameter space of the coarse-grained UNRES force field by random
414 search: selecting a transferable medium-resolution force field.
415 {\it J. Comput. Chem.}, {\bf 2009}, 30, 2127-2135.
417 \bibitem{kozlowska_2010}
418 U. Kozlowska, A. Liwo. H.A. Scheraga.
419 Determination of side-chain-rotamer and side-chain and backbone
420 virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
421 terminally-blocked amino-acid residues, for coarse-grained simulations of
422 protein structure and folding. 1. The Method.
423 {\it J. Comput. Chem.}, {\bf 2010}, 31, 1143-1153.
425 \bibitem{kozlowska_2010_02}
426 U. Kozlowska, G.G. Maisuradze, A. Liwo, H.A. Scheraga.
427 Determination of side-chain-rotamer and side-chain and backbone
428 virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
429 terminally-blocked amino-acid residues, for coarse-grained simulations of
430 protein structure and folding. 2. Results, comparison with statistical
431 potentials, and implementation in the UNRES force field.
432 {\it J. Comput. Chem.}, {\bf 2010}, 31, 1154-1167.
435 A. Liwo, S. Oldziej, C. Czaplewski, D.S. Kleinerman, P. Blood, H.A. Scheraga.
436 Implementation of molecular dynamics and its extensions with the coarse-grained
437 UNRES force field on massively parallel systems; towards millisecond-scale
438 simulations of protein structure, dynamics, and thermodynamics.
439 {\it J. Chem. Theory Comput.}, {\bf 2010}, 6, 890-909.
441 \bibitem{sieradzan_2012}
442 A.K. Sieradzan, U.H.E. Hansmann, H.A. Scheraga, A. Liwo.
443 Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
444 {\it J. Chem. Theory Comput.}, {\bf 2012}, 8, 4746-4757.
447 P. Krupa, A.K. Sieradzan, S. Rackovsky, M. Baranowski, S. O{\l}dziej,
448 H.A. Scheraga, A. Liwo, C. Czaplewski.
449 Improvement of the treatment of loop structures in the UNRES
450 force field by inclusion of coupling between backbone- and
451 side-chain-local conformational states
452 {\it J. Chem. Theory Comput.}, {\bf 2013}, 4620-4632.
454 \bibitem{sieradzan_2014}
455 A.K. Sieradzan, A. Niadzvedtski, H.A. Scheraga, A. Liwo.
456 Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino
457 acid residues in the coarse-grained united residue (UNRES) force field.
458 {\it J. Chem. Theory Comput.}, {\bf 2014}, 10, 2194-2203.
460 \bibitem{sieradzan_2015}
461 A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
462 Physics-based potentials for the coupling between backbone- and
463 side-chain-local conformational states in the united residue
464 (UNRES) force field for protein simulations.
465 {\it J. Chem. Theory Comput.}, {\bf 2015}, 11, 817-831.
468 P. Krupa, A. Ha"labis, W. "Rmudzi"nska, S. O"ldziej, H.A. Scheraga, A. Liwo.
469 Maximum Likelihood Calibration of the UNRES Force Field for
470 Simulation of Protein Structure and Dynamics.
471 \textit{J. Chem. Inf. Model}. \textbf{2017}, 57, 2364-2377
473 \bibitem{karczynska_2018}
474 A.S. Karczy"nska, M.A. Mozolewska, P. Krupa, A. Gie"ldo"n, A. Liwo, C. Czaplewski.
475 Prediction of protein structure with the coarse-grained UNRES
476 force field assisted by small X-ray scattering data and
477 knowledge-based information.
478 \textit{Proteins: Struct. Func. Bioinfo.}, \textbf{2018}, 86 (S1), 228-239. %DOI: 10.1002/prot.25421.
480 \bibitem{czaplewski_2018}
481 C. Czaplewski, A. Karczy"nska, A.K. Sieradzan, A. Liwo.
482 UNRES server for physics-based coarse-grained simulations and prediction
483 of protein structure, dynamics and thermodynamics.
484 \textit{Nucleic Acids Research}, \textbf{2018}, 46, W304-W309.
486 \end{thebibliography}
491 \section{INSTALLATION}
494 Please follow the instructions in the installation guide to download and put the package on your
495 system. In what follows, \$UNRESROOT is the location of the UNRES package in your system.
497 It is recommended to install all components of the package using the Cmake utility.
498 Please follow the instructions in the installation guide.
500 This section describes the installation of only the UNRES component of the package,
501 using make program. Sample Makefiles are present in the respective source directories.
503 To produce the executable do the following:
505 \begin{enumerate}[(a)]
508 To build parallel version, make sure that MPI is installed in your system.
509 Note that the package will have limited functions when compiled in a single-CPU mode.
510 On linux cluster the command source \$HOME/.env should be added to .tcshrc
511 or equivalent file to use parallel version of the program, the
512 alternative is to use queuing system like PBS.
513 In some cases the FORTRAN library subroutine GETENV does not work properly
514 with MPI, if the script is run interactively. In such a case try to
515 add the source mygentenv.F and turn on the -DMYGETENV preprocessor flag.
518 Change directory to the respective source directory.
521 Select the appropriate Makefile\_xxxx or copy the most matching Makefile\_xxx
522 to another name (e.g., Makefile\_MySystem) and edit it to customize to your
523 system. Note that the CSA version works only with MPI.
525 Makefile\_pgf90 - Linux, the pgf90 compiler,
526 Makefile\_intel - Linux, Intel Fortran compiler,
527 Makefile\_gfortran - Gnu Fortran compiler,
528 Makefile\_bluegene - BlueGene/Q (AIX Fortan).
531 Please note that Makefile must be a symbolic link to the Makefile\_xxx of choice. Make sure
532 that the file cinfo.f is present; if not, execute:
539 Other systems should not cause problems; all you have to do is to change
540 the compiler, compiler options, and preprocessor options.
542 By default, the executables will be placed in \$UNRESROOT/bin/unres/CSA
543 \$UNRESROOT/bin/unres/MD and UNRES/bin/unres/MINIM, respectively.
545 The following architectures are defined in the .F source files:
549 \item{AIX} -- AIX systems (put -DAIX as one of the preprocessor options, if
550 this is your system).
552 \item{LINUX} -- Linux (put -DLINUX).
554 \item{G77} -- Gnu-Fortran compilers (might require sum moderate source code editing)
555 (put -DG77). The recommended compiler is gfortran and not g77.
557 \item{PGI} -- PGI compilers.
559 \item{WINPGI} -- additional setting for PGI compilers for MS Windows.
561 \item{SGI} -- all SGI platforms; should also be good for SUN platforms (put -DSGI).
563 \item{CRAY} -- handles some Cray-specific I/Os and other instructions.
565 \item{WIN} -- MS Windows with Digital Fortran compiler (put -DWIN)
569 For other platforms, the only problems might appear in connection with
570 machine-specific I/O instructions. Many files are opened in the append
571 mode, whose specification in the OPEN statement is quite machine-dependent.
572 In this case you might need to modify the source code accordingly.
573 The other platform dependent routines are the timing routines contained
574 in timing.F. In addition to the platforms specified above, ES9000, SUN,
575 KSR, and CRAY are defined there.
577 For parallel build -DMP and -DMPI must be set (these are set in Makefile).
579 IMPORTANT! Apart from this, two define flags: -DCRYST\_TOR and -DMOMENT
580 define earlier versions of the force field. The MUST NOT be entered, if
581 the CASP5 and later versions of the force field are used.
585 Build the unres executables by typing at your UNIX prompt:
588 make # will build unres
589 make clean # will remove the object files
592 The bin directory contains pre-built binaries for Red Hat Linux. These
593 executables are specified in the csh scripts listed in section 4.
597 Customize the C-shell scripts unres.unres (to run the parallel version on
598 set of workstation). See the next section of this manual for guidance.
600 After the executables are build and C-shell scripts customized, you can run the
601 test examples contained in UNRES/examples.
607 \section{CUSTOMIZING YOUR C-SHELL SCRIPT}
610 IMPORTANT NOTE -- The unres.csh script is for Linux and should also be easily
611 adaptable to other systems running MPICH. This script is for interactive
612 parallel jobs. Examples of scripts compatible with PBS (pbs.sub) and LoadLever
613 (sp2.sub) queuing systems are also provided.
615 Edit the following lines in your unres.csh script:
618 set DD = your_database_directory
621 e.g., if you installed the package on the directory /usr/local, this line
625 set DD = /usr/local/UNRES/PARAM
626 set BIN = your_binaries_directory
627 set FGPROCS = number_of_processors_per_energy/force_evaluation (MD)
630 e.g., if the root directory is as above:
633 set BIN = /usr/local/UNRES/bin
636 \section{COMMAND LINE AND FILES}
639 To run UNRES interactively enter the following command at your Unix prompt
640 or put it in the batch script:
643 unres.csh POTENTIAL INPUT N_PROCS
648 POTENTIAL specifies the side-chain interaction potential type and must be
649 one of the following:
653 \item{LJ} -- 6-12 radial Lennard-Jones.
655 \item{LJK} -- 6-12 radial Lennard-Jones-Kihara (shifted Lennard Jones).
657 \item{BP} -- 6-12 anisotropic Berne-Pechukas based on Gaussian overlap (dilated
660 \item{GB} -- 6-12 anisotropic Gay-Berne (shifted Lennard-Jones).
662 \item{GBV} -- 6-12 anisotropic Gay-Berne-Vorobjev (shifted Lennard-Jones).
664 See section \ref{sect:forcefields} (Force Fields) for explanation and usage.
666 At present, only the LJ and GB potentials are applied. The LJ potential
667 is used in the ``CASP3'' version of the UNRES force field that is able
668 to predict only $\alpha$-helical structures. All further version of the
669 UNRES force field use the GB potential. For the description of all above-mentioned
670 potentials see ref. \cite{liwo_1997_02}.
672 \item{INPUT} is the prefix for input and output files (see below)
674 \item{N\_PROCS} is the number of processors; for a CSA or REMD/MREMD run it MUST be at least 2.
678 Note! The script takes one more variable, FGPROCS, as the fourth argument,
679 which is the number of fine-grain processors to parallelize energy
680 evaluations. The corresponding code is in UNRES/CSA, but it was written
681 using MPL instead of MPI and therefore is never used in the present version.
682 At present we have no plans to rewrite fine-grain parallelization using MPI,
683 because we found that the scalability for up to 200 residue polypeptide
684 chains was very poor, due to a small number of interactions and,
685 correspondingly, unfavorable ratio of the overhead to the computation time.
689 \item{INPUT.inp} contains the main input data and the control parameters of the CSA
692 \item{INPUT.out\_POTENTIAL\_xxx} is the main output files from different processors; xxx
693 denotes the number of the processor
695 \item{INPUT\_POTENTIALxxx.stat} is the summary files with the energies, energy components,
696 and RMS deviations of the conformations produced by each of the processors;
697 not used in CSA runs; also it outputs different quantity in MD/MREMD runs.
699 CSA version specific files:
701 \item{INPUT\_POTENTIALxxx.int} is the internal coordinates; in the CSA run
703 \item{INPUT\_POTENTIAL\_000.int} contains the coordinates of the conformations,
704 and the other files are empty
706 \item{INPUT.CSA.history} is the history file from a CSA run. This is an I/O file, because
707 it can be used to restart an interrupted CSA run.
709 \item{INPUT.CSA.seed} stores the random seed generated in a CSA run; written for
712 \item{INPUT.CSA.bank} is the current bank of conformations obtained in CSA calculations
713 (expressed as internal coordinates). This information is also stored in
714 INPUT\_POTENTIAL000.int
716 \item{INPUT.CSA.rbank} -- as above, but contains random-generated conformations.
720 MD version specific files:
724 \item{INPUT\_MDyyy.pdb} is the Cartesian coordinates of the conformations in PDB format.
726 \item{INPUT\_MDyyy.x} is the Cartesian coordinates of the conformations in ASCII format.
728 \item{INPUT\_MDyyy.cx} is the Cartesian coordinates of the conformations in compressed format
729 (need xdr2pdb to convert to PDB format).
732 The program currently produces some more files, but they are not used
733 for any purposes and most of them are scratched after a run is completed.
735 The run script also contains definitions of the parameter files through the
736 following environmental variables:
740 \item{SIDEPAR} -- parameters of the SC-SC interaction potentials ($U_{SC SC}$);
742 \item{SCPPAR} -- parameters of the SC-p interaction potential ($U_{SCp}$); this file can
743 be ignored by specifying the -DOLDSCP preprocessor flag, which means that the
744 built-in parameters are used; at present they are the same as the parameters
745 in the file specified by SCPPAR;
747 \item{ELEPAR} -- parameters of the p-p interaction potentials ($U_{pp}$);
749 \item{FOURIER} -- parameters of the multibody potentials of the coupling between the
750 backbone-local and backbone-electrostatic interactions ($U_{corr}$);
752 \item{THETPAR} -- parameters of the virtual-bond-angle bending potentials ($U_b$);
754 \item{ROTPAR} -- parameters of the side-chain rotamer potentials ($U_{rot}$);
756 \item{TORPAR} -- parameters of the torsional potentials ($U_{rot}$);
758 \item{TORDPAR} -- parameters of the double-torsional potentials.
760 \item{SCCORPAR} -- parameters of the torsional potentials that account for the
761 coupling between the local backbone and local sidechain states (implemented recently).
767 \section{FORCE FIELDS}
768 \label{sect:forcefields}
770 UNRES is being developed since 1997 and several versions of the force field
771 were produced. The settings and references to these force fields are
774 Force fields for CSA version (can be used in MD but haven't been parameterized for this
778 \hspace{-2cm}\begin{longtable}{|l|l|l|l|l|l|l|}\hline
780 %---------------------------------------------------------------------------------------
781 & Additional & SC-SC & Example script & Structural &\\
782 Force field & compiler flags& potential& and executables & classes covered& References\\
783 & & & (Linux; PGF90 &&\\
784 & & & and IFC) &&\\ \hline
785 %---------------------------------------------------------------------------------------
786 CASP3 & -DCRYST\_TOR & LJ & unres\_CASP3.csh &only $\alpha$ &\cite{liwo_1997,liwo_1997_02,liwo_1998}\\
787 & -DCRYST\_BOND & &unres\_pgf90\_cryst\_tor.exe&&\\
788 & -DCRYST\_THETA & &unres\_ifc6\_cryst\_tor.exe &&\\
792 ALPHA & -DMOMENT & GB & unres\_CASP4.csh &only $\alpha$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
793 & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
794 & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
797 BETA & -DMOMENT & GB & unres\_CASP4.csh &only $\beta$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
798 & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
799 & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
802 ALPHABETA & -DMOMENT & GB & unres\_CASP4.csh & all &\cite{liwo_2001,lee_2001,pillardy_2001}\\
803 & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
804 & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
807 CASP5 & -DCRYST\_BOND & GB & unres\_CASP5.csh & all &\cite{liwo_2002,saunders_2003,saunders_2003_02,liwo_2004}\\
808 & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
809 & -DCRYST\_SC & & unres\_ifc6.exe &&\\
811 3P & -DCRYST\_BOND & GB & unres\_3P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
812 & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
813 & -DCRYST\_SC & & unres\_ifc6.exe &&\\
815 4P & -DCRYST\_BOND & GB & unees\_4P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
816 & -DCRYST\_THETA & & unres\_pgf90.exe&&\\
817 & -DCRYST\_SC & & unres\_ifc6.exe&&\\ \hline
818 %---------------------------------------------------------------------------------------
824 Force fields for MD version \cite{khalili_2005,khalili_2005_02}.
827 \begin{longtable}{|l|l|l|l|l|l|l|}\hline
828 %---------------------------------------------------------------------------------------
829 & Additional & SC-SC & Example script & Structural &\\
830 Force field & compiler flags& potential& and executables & classes covered& References\\
831 & & & (Linux; PGF90&&\\
832 & & & and IFC)&&\\ \hline
833 %---------------------------------------------------------------------------------------
834 GAB & -DCRYST\_BOND & GB & unres\_GAB.csh & mostly $\alpha$ & \cite{liwo_2007}\\
835 & -DCRYST\_THETA &&&&\\
839 E0G & -DCRYST\_BOND & GB & unres\_E0G.csh & mostly $\alpha$ & \cite{liwo_2007}\\
840 & -DCRYST\_THET &&&&\\
844 E0LL2Y &-DPROCOR & GB & unres\_ab.csh & all & \cite{liwo_2007,kozlowska_2007,he_2009,kozlowska_2010,kozlowska_2010_02}\\ \hline
845 %---------------------------------------------------------------------------------------
849 The example scripts (the *.csh filed) contain all appropriate parameter files, while
850 the energy-term weights are provided in the example input files listed in EXAMPLES.TXT
851 (*.inp; see section \ref{sect:input}. for description of the input files). However, it is user's
852 responsibility to specify appropriate compiler flags. Note that a version WILL NOT work,
853 if the force-field specific compiler flags are not set. The parameter files specified
854 in the run script also must strictly correspond to the energy-term weights specified in
855 the input file. The parameter files for specific force fields are also specified below
856 and the energy-term weights are specified in section \ref{sect:input}.
858 The parameter files are as follows (the environment variables from section \ref{sect:command} are
859 used to identify the parameters):
863 \begin{longtable}{ll}
864 BONDPAR &bond.parm \\
865 THETPAR &thetaml.5parm\\
866 ROTPAR &scgauss.parm\\
867 TORPAR &torsion\_cryst.parm\\
868 TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
869 SIDEPAR &scinter\_LJ.parm\\
870 ELEPAR &electr.parm\\
872 FOURIER &fourier\_GAP.parm (not used)\\
873 SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
876 ALPHA, BETA, ALPHABETA (CASP4):
878 \begin{longtable}{ll}
879 BONDPAR &bond.parm \\
880 THETPAR &thetaml.5parm\\
881 ROTPAR &scgauss.parm\\
882 TORPAR &torsion\_ecepp.parm\\
883 TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
884 SIDEPAR &scinter\_GB.parm\\
885 ELEPAR &electr.parm\\
887 FOURIER &fourier\_GAP.parm\\
888 SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
893 \begin{longtable}{ll}
895 THETPAR &thetaml.5parm\\
896 ROTPAR &scgauss.parm\\
897 TORPAR &torsion\_631Gdp.parm\\
898 TORDPAR &torsion\_double\_631Gdp.parm\\
899 SIDEPAR &scinter\_GB.parm\\
900 ELEPAR &electr\_631Gdp.parm\\
902 FOURIER &fourier\_opt.parm.1igd\_iter7n\_c\\
903 SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
908 \begin{longtable}{ll}
910 THETPAR &thetaml.5parm\\
911 ROTPAR &scgauss.parm\\
912 TORPAR &torsion\_631Gdp.parm\\
913 TORDPAR &torsion\_double\_631Gdp.parm\\
914 SIDEPAR &sc\_GB\_opt.3P7\_iter81\_1r\\
915 ELEPAR &electr\_631Gdp.parm\\
917 FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
918 SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
923 \begin{longtable}{ll}
925 THETPAR &thetaml.5parm\\
926 ROTPAR &scgauss.parm\\
927 TORPAR &torsion\_631Gdp.parm\\
928 TORDPAR &torsion\_double\_631Gdp.parm\\
929 SIDEPAR &sc\_GB\_opt.4P5\_iter33\_3r\\
930 ELEPAR &electr\_631Gdp.parm\\
932 FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
933 SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
938 \begin{longtable}{ll}
940 THETPAR &thetaml.5parm\\
941 ROTPAR &scgauss.parm\\
942 TORPAR &torsion\_631Gdp.parm\\
943 TORDPAR &torsion\_double\_631Gdp.parm\\
944 SIDEPAR &sc\_GB\_opt.1gab\_3S\_qclass5no310-shan2-sc-16-10-8k\\
945 ELEPAR &electr\_631Gdp.parm\\
947 FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
948 SCCORPAR&sccor\_pdb\_shelly.dat\\
953 \begin{longtable}{ll}
955 THETPAR &thetaml.5parm\\
956 ROTPAR &scgauss.parm\\
957 TORPAR &torsion\_631Gdp.parm\\
958 TORDPAR &torsion\_double\_631Gdp.parm\\
959 SIDEPAR &sc\_GB\_opt.1e0g-52-17k-2k-newclass-shan1e9\_gap8g-sc\\
960 ELEPAR &electr\_631Gdp.parm\\
962 FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
963 SCCORPAR&sccor\_pdb\_shelly.dat\\
968 \begin{longtable}{ll}
969 BONDPAR &bond\_AM1.parm\\
970 THETPAR &theta\_abinitio.parm\\
971 ROTPAR &rotamers\_AM1\_aura.10022007.parm\\
972 TORPAR &torsion\_631Gdp.parm\\
973 TORDPAR &torsion\_double\_631Gdp.parm\\
974 SIDEPAR &scinter\_\${POT}.parm\\
975 ELEPAR &electr\_631Gdp.parm\\
977 FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
978 SCCORPAR&sccor\_am1\_pawel.dat\\
981 Additionally, for E0LL2Y, the following environment variables and files are required
982 to generate random conformations:
984 THETPARPDB thetaml.5parm\\
985 ROTPARPDB scgauss.parm
987 For CSA, the best force field is 4P. For MD, the E0LL2Y force field is best for
988 ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
989 overemphasizes $\beta$-structures and has to be run with secondary-structure-prediction
990 information. For prediction of the structure of mostly $\alpha$-protein, and for running
991 dynamics of large proteins, the best is the GAB force field. All these force fields
992 were trained by using our procedure of hierarchical optimization \cite{oldziej_2004,oldziej_2004_02}.
993 The 4P and E0LL2Y force fields have considerable power independent of structural class.
994 The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
995 and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
996 predicts reasonably the structure of $\alpha$-helical proteins and is still not obsolete,
997 while for $\beta$- and $\alpha+\beta$-structure prediction
998 3P or 4P should be used, because they are cheaper and more reliable than BETA and
999 ALPHABETA. The early CASP3 force field is included for historical reasons only.
1003 \section{INPUT FILES}
1006 \subsection{Main input data file}
1007 \label{sect:input:main}
1009 Most of the data are organized as data lists, where the data can be put
1010 in any order, using a series of statements of the form:
1014 for simple non-logical variables
1020 to indicate that the corresponding option is turned on. For array variables
1021 the assignment statement is:
1023 KEYWORD=value1,value2,...
1025 However, the data lists are unnamed and that must be placed EXACTLY in the
1026 order indicated below. The presence of an \& in the 80th column of a line
1027 indicates that the next line will belong to the same data group. The parser
1028 subroutines that interpret the keywords are case insensitive.
1030 Each group of data organized as a data list is indicated as data list format
1033 \subsubsection{Title}
1034 \label{sect:input:main:title}
1036 Any string containing up to 80 characters. The first input line is always
1037 interpreted as title.
1039 \subsubsection{Control data}
1040 \label{sect:input:main:control}
1042 This data section is in data list format and is read in the READ\_CONTROL subroutine.
1044 \paragraph{Keywords to chose calculation type}
1048 \item{TIMLIM} -- time limit in minutes (960)
1050 %\item{OUT1FILE} -- only the master processor prints the output file in a parallel job
1052 \item{MINIMIZE} -- if present, energy minimization will be carried out.
1054 \item{REGULAR} -- regularize the read in conformation (usually a crystal or
1055 NMR structure) by doing a series of three constrained minimizations,
1056 to keep the structure as close as possible to the starting
1057 (experimental) structure. The constraints are the CA-CA distances
1058 of the initial structure. The constraints are gradually diminished
1059 and removed in the last minimization.
1061 \item{SOFTREG} -- regularize the read in conformation (usually a crystal or NMR
1062 structure) by doing a series of constrained minimizations, with
1063 additional use of soft potential and secondary structure
1064 freezing, to keep the structure as close as possible to the
1065 starting (experimental) structure.
1068 \item{CSA} -- if present, the run is a CSA run. At present, this is the only
1069 reliable mode of doing global conformational search with this
1070 package; it is NOT recommended to use MCM or THREAD for this
1073 \item{MCM} -- if present, this is a Monte Carlo Minimization (MCM) run.
1075 \item{MULTCONF} -- if present, conformations will be read from the INPUT.intin
1078 \item{MD} -- run canonical MD (single or multiple trajectories).
1080 \item{RE} -- run REMD or MREMD (parallel jobs only).
1082 \item{MUCA} -- run multicanonical MD calculations (parallel jobs only).
1084 \item{MAP=number} (integer) --
1085 Conformational map will be calculated in chosen angles.
1087 \item{THREAD=number} (integer) --
1088 Threading or threading-with-minimization run, using a database of structures
1089 contained in the \$DD/patterns.cart pattern data base (502 chains or chain
1090 fragments), using a total number patterns. It is recommended to use this with
1091 energy minimization; this implies regularization of each minimized pattern.
1092 See refs. \cite{liwo_1997_02} and \cite{liwo_1997_03}.
1094 \item{CHECKGRAD} -- compare numerical and analytical gradient; to be followed by:
1096 \item{CART} -- energy gradient in virtual-bond vectors (Cartesian coordinates)
1098 \item{INT} -- energy gradient in internal coordinates (default)
1100 \item{CARINT} -- derivatives of the internal coordinates in the virtual-bond vectors.
1104 \paragraph{Specification of protein and structure output in non-MD applications}
1108 \item{ONE\_LETTER} -- one-letter and not three-letter code of the amino-acid residues
1111 \item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
1113 \item{PDBSTART} -- the initial conformation is read in from a PDB file.
1115 \item{UNRES\_PDB} -- the starting conformation is in UNRES representation (C$^\alpha$
1116 and SC coordinates only). This keyword MUST appear in such a case
1117 or the program will generate erroneous and unrealistic side-chain
1120 \item{RAND\_CONF} -- start from a random conformation.
1122 \item{EXTCONF} -- start from an extended chain conformation.
1124 \item{PDBOUT} -- if present, conformations will be output in PDB format. Note that
1125 this keyword affects only the output from single energy evaluation,
1126 energy minimization and multiple-conformation data. To request
1127 conformations from MD/MREMD runs in PDB format, the MDPDB keyword
1128 must be placed on the MD input record.
1130 \item{MOL2OUT} -- if present, conformations will be output in SYBYL mol2 format.
1132 \item{REFSTR} -- if present, reference structure will be read (e.g., to monitor
1133 the RMS deviation from the crystal structure).
1135 \item{PDBREF} -- if present, a reference structure will be read in to compare
1136 the calculated conformations with it.
1138 \item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
1141 \item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
1142 restraints (to be included in further section of the input).
1144 \item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
1146 \item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
1150 Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
1151 Output mode for MD version is specified in MD input (see section \ref{sect:input:main:MD}).
1153 \paragraph{Miscellaneous}
1157 \item{CONSTR\_DIST=number}
1160 \item{0} -- no distance restraints,
1161 \item{$>0$} -- imposes harmonic restraints on selected distances; see section 5.12.
1162 In MD version, also restraints on the q variable \cite{liwo_2007} can be used.
1165 \item{WEIDIS=number} (real)
1166 the weight of the distance term; applies for REGULARIZE and THREAD, otherwise
1169 \item{USE\_SEC\_PRED} -- use secondary-structure prediction information.
1171 \item{SEED=number} (integer) (no default)
1172 Random seed (required, even if the run is not a CSA, MCM, MD or MREMD run).
1174 \item{PHI} -- only the virtual-bond dihedral angles $\gamma$ are considered as
1175 variables in energy minimization.
1177 \item{BACK} -- only the backbone virtual angles (virtual-bond angles theta and
1178 virtual-bond dihedral angles $\gamma$) are considered as variables
1179 in energy minimization.
1181 By default, all internal coordinates: $\theta$, $\gamma$, and the side-chain
1182 centroid polar angles $\alpha$ and $\beta$ are considered as variables in energy
1185 \item{RESCALE\_MODE=number} (real)
1186 Choice of the type of temperature dependence of the force field.
1188 \item{0} -- no temperature dependence
1189 \item{1} -- homographic dependence (not implemented yet with any force field)
1190 \item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
1193 \item{T\_BATH=number} (real)
1194 temperature (for MD runs and temperature-dependent force fields).
1197 The following keywords apply to MCM only:
1201 \item{MAXGEN=number} (integer) (10000)
1202 maximum number of conformations generated in a single MCM iteration
1204 \item{MAXOVERLAP=number} (integer) (1000)
1205 maximum number of conformations with ``bad'' overlaps allowed to appear in a
1206 row in a single MCM iteration.
1208 \item{DISTCHAINMAX} -- (multi-chain capacity only) maximum distance between the
1209 last residue of a given chain and the first residue of the
1210 next chain such that restraints will not be imposed; quartic
1211 restraints will be imposed for greater distances.
1213 \item{ENERGY\_DEC} -- detailed energies will be printed for each interacting pair
1214 or each virtual bond, virtual-bond angle and dihedral angle,
1215 side chain, etc. DO NOT use unless a single energy evaluation
1219 \subsubsection{Minimizer options}
1221 This data section is in data list format and is read in the READ\_MINIM subroutine.
1223 This data group is present, if MINIMIZE was specified on the control card.
1224 Otherwise, it must not appear.
1228 \item{CART} -- minimize in virtual-bond vectors instead of angles.
1230 \item{MAXMIN=number} (integer) (2000)
1231 maximum number of iterations of the SUMSL minimizer.
1233 \item{MAXFUN=number} (integer) (5000)
1234 maximum number of function evaluations in a single minimization.
1236 \item{TOLF=number} (real) (1.0e-2)
1237 Tolerance on function.
1239 \item{RTOLF=number} (real) (1.0d-4)
1240 Relative tolerance on function.
1242 \item{PRINT\_INI} -- turns on printing nondefault minimization parameters,
1243 initial variables, and gradients in the SUMSL procedures.
1245 \item{PRINT\_FINAL} -- turns on printing final variables and gradients in
1248 \item{PRINT\_STAT} -- turns on printing abbreviated minimization protocol.
1252 The SUMSL minimizer is used in UNRES/CSA. For detailed description of
1253 the control parameters see the source file cored.f and sumsld.f
1256 \subsubsection{CSA control parameters}
1257 \label{sect:input:main:CSA}
1259 This data group should be present only, if CSA was specified on the control
1260 card. It is recommended that the readers to read publications on CSA method
1261 for more complete description of the parameters. Brief description of
1266 \item{NCONF=number} (integer) (50)
1267 This corresponds to the size of the bank at the beginning of the
1268 CSA procedure. The size of the bank, nbank, is set to nconf.
1269 If necessary (at much later stages of the CSA: see icmax below),
1270 nbank increases by multiple of nconf.
1272 \item{JSTART=number} (integer) (1)
1274 \item{JEND}=number (integer) (1)
1275 This corresponds to the limit values of do loop, each of which
1276 corresponds to an separate CSA run. If jstart=1, and jstart=100,
1277 this routine will repeat 100 separate CSA runs (limited by CPU)
1278 each one with separate random number initialization.
1279 The only difference between two CSA runs (one with jstart=jend=1
1280 and another one with jstart=jend=2) would be different random
1281 number initializations if other parameters are identical.
1283 \item{NSTMAX=number} (integer) (500000)
1284 This is to set a limit the total number of local minimizations of CSA
1289 N1=number (integer) (6)\\
1290 N2=number (integer) (4)\\
1291 N3=number (integer) (0)\\
1292 N4=number (integer) (0)\\
1293 N5=number (integer) (0)\\
1294 N6=number (integer) (10)\\
1295 N7=number (integer) (0)\\
1296 N8=number (integer) (0)\\
1297 N9=number (integer) (0)\\
1298 IS1=number (integer) (1)\\
1299 IS2=number (integer) (8)\\
1301 These numbers are used to generate trial conformations for each seed.
1302 See the file newconf.f for more details.
1305 \item{n1:} the total number of trial conformations for each seed by substituting
1306 nran number of variable angles (see subroutine newconf1ab and
1307 subroutine newconf1ar),
1308 \item{n2:} the total number of trial conformations for each seed by substituting
1309 nran number of groups of variable angles (see subroutine newconf1bb and
1310 subroutine newconf1br),
1311 \item{n3:} the total number of trial conformations for each seed by substituting
1312 a window of residues which forms a $\beta$-hairpin, if there is no enough
1313 $\beta$-hairpins uses the same algorithm as n6,
1314 \item{n4:} the total number of trial conformations for each seed by shifting the
1315 turn in $\beta$-hairpin by +/- 1 or 2 residues, if there is no enough
1316 $\beta$-hairpins uses the same algorithm as n6,
1317 \item{n5:} not used,
1318 \item{n6:} the total number of trial conformations for each seed by substituting
1319 a window of residues [is1,is2] inclusive. The size of the window is
1320 determined in a random fashion (see subroutine newconf\_residue for
1321 generation of the trial conformations),
1322 \item{n7:} the total number of trial conformations for each seed by copying a
1323 remote strand pair forming nonlocal $\beta$-sheet contact,
1324 \item{n8:} the total number of trial conformations for each seed by copying an
1325 $\alpha$-helical segment,
1326 \item{n9:} the total number of trial conformations for each seed by shifting the
1327 $\alpha$-helical segment by +/- 1 or 2 residues.
1330 Typical values used for a 75-residue helical protein is
1331 (6 4 0 0 0 10 1 26) for (n1,n2,n3,n4,n5,n6,is1,is2), respectively.
1332 In this example, a total of 20 trial conformations are generated for a seed
1333 Usually is1=1 is used for all applications, and the value of is2 is set about
1334 to 1/3 of the total number of residues. n3, n4 and n7 are design to help in
1335 case of proteins with $\beta$-sheets
1337 NRAN0=number (integer) (4)\\
1338 NRAN1=number (integer) (2)\\
1339 IRR=number (integer) (1)\\
1341 These numbers are used to determine if the CSA stage is very early.
1342 One can use (4 2 1) for these values. For more details one should look into
1343 the file, newconf.f, for more details.
1345 NTOTAL=number (integer) (10000)\\
1346 CUT1=number (real) (2.0)\\
1347 CUT2=number (real) (5.0)\\
1349 Annealing schedule is set in following fashion.
1350 The value of D\_cut is reduced geometrically from 1/cut1 of D\_ave (at the
1351 beginning) to 1/cut2 of D\_ave (after ntotal number of minimizations) where
1352 D\_ave is the average distance between two conformations in the First\_bank.
1356 \item{ESTOP=number} (real) (-3000.0)
1357 The CSA procedure stops if a conformations with energy lower than estop is
1358 obtained. If the do-loop set by jstart and jend requires more than one loop,
1359 the program will go on until the do-loop is finished.
1361 \item{ICMAX=number} (integer) (3)
1362 The maximum value of cycle (see the original publications for details).
1363 If the number of cycle exceeds this value the program will add nconf
1364 more conformations to Bank and First\_bank to continue CSA procedure if
1365 the new size of the nbank is within the maximum set by nbankm (see above).
1366 If the size of nbank exceeds the maximum set by nbankm the CSA procedure
1367 for this run will stop and next CSA will begin depending on the do-loop
1368 set by jstart and jend.
1370 \item{IRESTART=number} (integer) (0)
1371 This tells you if the run is fresh start (irestart=0) or a restart (irestart=1)
1372 starting from an old results
1374 \item{NDIFF=number} (integer) (2)
1375 The number of variables use in comparison when structure is added to the
1376 bank,4 - all angels, 2 - only backbone angles $\gamma$ and $\theta$
1378 \item{NBANKTM=number} (integer) (0)
1379 The maximum number of structures saved in *.CSA.bankt as history of the run
1380 Do not use bankt on massively parallel computation as it kills scalability.
1382 \item{DELE=number} (real) (20.0)
1383 Energy cutoff for bankt.
1385 \item{DIFCUT=number} (real) (720.0)
1386 Angle cutoff for bankt.
1388 \item{IREF=number} (integer) (0)
1389 0 - normal run, 1 - local CSA which generates only structures close to the
1390 reference one read from *.CSA.native.int file.
1392 \item{RMSCUT=number} (real) (4.0)
1393 CA RMSD cut off used in local CSA
1395 \item{PNCCUT=number} (real) (0.5)
1396 Percentage of native contact used in local CSA
1398 \item{NCONF\_IN=number} (integer) (0)
1399 The number of conformation read for the first bank from the input file
1403 Optionally, the CSA parameters can be read from file INPUT.CSA.in, if
1404 this file exists. If so, they are read in free format in the following
1410 n1,n2,n3,n4,n5,n6,n7,n8,is1,is2\\
1416 ntbankm,dele,difcut\\
1417 iref,rmscut,pnccut\\
1421 \subsubsection{MCM data}
1422 \label{sect:input:main:MCM}
1424 (Data list format, subroutine MCMREAD.)
1426 This data group is present, if MCM was specified on the control card.
1427 Otherwise it must not appear.
1431 \item{MAXACC=number} (integer) (100)
1432 Maximum number of accepted conformations.
1434 \item{MAXTRIAL=number} (integer) (100)
1435 Maximum number of unsuccessful trials in a row.
1437 \item{MAXTRIAL\_ITER=number} (integer) (1000)
1438 Maximum number of unsuccessful trials in a single iteration.
1440 \item{MAXREPM=number} (integer) (200)
1441 Maximum number of repetitions of the same minimum.
1443 \item{RANFRACT=number} (real) (0.5d0)
1444 Fraction of chain-rebuild motions.
1446 \item{OVERLAP=number} (real) (1.0d3)
1447 Bad contact energy criterion.
1449 \item{NSTEPH=number} (integer) (0)
1450 Number of heating step in adaptive sampling.
1452 \item{NSTEPC=number} (integer) (0)
1453 Number of cooling step in adaptive sampling.
1455 \item{TMIN=number} (real) (298.0d0)
1456 Minimum temperature in adaptive-temperature sampling).
1458 \item{TMAX=number} (real) (298.0d0)
1459 Maximum temperature in adaptive-temperature sampling).
1461 The temperature is changed according to the formula:
1463 T = TMIN*EXP(ISTEPH*(TMAX-TMIN)/NSTEPH) when heating
1467 T = TMAX*EXP(-ISTEPC*(TMAX-TMIN)/NSTEPC) when cooling
1469 The default is to use a constant temperature.
1471 \item{NWINDOW=number} (integer) (0)
1472 Number of windows in which the variables will be perturbed; the windows are
1473 defined by the numbers of the respective amino-acid residues. If NWINDOW
1474 is nonzero, after specifying all MCM input the next lines must define the
1475 windows. Each line looks like this:
1477 winstart winend (free format)
1479 e.g. if NWINDOW=2, the input:
1484 will mean that only the variables of residues 4-10 and 15-20 will be perturbed.
1485 However, in general, all variables will be considered in minimization.
1487 \item{PRINT\_MC=number} (0)
1488 Printout level in MCM. 0 - no intermediate printing, 1 and 2 - moderate
1489 printing, 3 - extensive printing.
1491 \item{NO\_PRINT\_STAT} -- no output to INPUT\_POTENTIALxxx.stat.
1493 \item{NO\_PRINT\_INT} -- no internal-coordinate output to INPUT\_POTENTIALxxx.int.
1497 \subsubsection{MD data}
1498 \label{sect:input:main:MD}
1500 (Mixed format; subroutine READ\_MDPAR.)
1504 \item{NSTEP} (1000000) number of time steps per trajectory.
1506 \item{NTWE} (100) NTWX (1000) frequency of energy and coordinate output, respectively.
1507 The coordinates are dumped in the pdb or compressed Gromacs (cx) format,
1508 depending on the next keyword.
1509 NTWE=0 means no energy dump.
1511 \item{MDPDB} - dump coordinates in the PDB format (cx otherwise)
1513 \item{TRAJ1FILE} only the master processor outputs coordinates. This feature pertains
1514 only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
1517 \item{REST1FILE} only the master writes the restart file
1519 \item{DT} (real) (0.1) time step; the unit is ``molecular time unit'' (mtu); 1 mtu = 48.9 fs
1521 \item{DAMAX} (real) (1.0) maximum allowed change of acceleration during a single time step.
1522 The time step gets scaled down, if this is exceeded.
1524 \item{DVMAX} (real) (20.0) -- maximum allowed velocity (in A/mtu)
1526 \item{EDRIFTMAX} (real) (10.0) -- maximum allowed energy drift in a single MD step (10 kcal/mol)
1528 \item{REST} -- restart flag. The calculation is restarted if present.
1530 \item{LARGE} -- very detailed output. Don't use except for debugging.
1532 \item{PRINT\_COMPON} -- prints energy components.
1534 \item{RESET\_MOMENT} (1000) -- frequency of zeroing out the total angular momentum when
1535 running Berendsen mode calculations (for Langevin calculations meaningless).
1537 \item{RESET\_VEL}=number (integer) (1000) -- frequency of resetting velocities to values
1538 from Gaussian distribution.
1540 \item{RATTLE} -- use the RATTLE algorithm (constraint bonds); not yet implemented.
1542 \item{RESPA} -- use the Multiple Time Step (MTS) or Adaptive Multiple Time Step (A-MTS)
1543 algorithm \cite{rakowski_2006}. Without this flag the variable time step (VTS) \cite{khalili_2005} is run.
1545 \item{NTIME\_SPLIT=number} (integer) (1) -- initial number of time-split steps
1547 \item{MAXTIME\_SPLIT=number} (integer) (64) -- maximum number of time-split step
1549 If NTIME\_SPLIT==MAXTIME\_SPLIT, MTS is run.
1551 \item{R\_CUT=number} (real) (2.0) -- the cut-off distance in splitting the forces into short- and
1552 long-range in site-site VDW distance units.
1554 \item{LAMBDA} (real) (0.3) -- the transition length (in site-site VDW distance units) between
1555 short- and long-range forces.
1557 \item{XIRESP} -- flag to use MTS/A-MTS with Nos\'e-Hoover/Nos\'e-Poincar\'e thermostats.
1559 \item{LANG=number} (integer) (0) Langevin dynamics flag:
1562 \item{0} -- No explicit Langevin dynamics.
1563 \item{1} -- Langevin with direct integration of the equations of motion (recommended
1564 for Langevin calculations)
1565 \item{2} -- Langevin calculation with analytical pre-integration of the friction and
1566 stochastic part of the equations of motion using an algorithm adapted from TINKER.
1567 This is MUCH MORE time- and memory-consuming than 1 and requires compiling without
1568 the -DLANG0 flag and enormously increases memory requirements.
1569 \item{3} -- The stochastic integrator developed by Cicotti and coworkers.
1570 \item{4} -- for other stochastic integrators (not used at present).
1573 Note: With the enclosed code, the -DLANG0 compiler flag is included which disables
1576 \item{TBF} -- Berendsen thermostat.
1578 \item{TAU\_BATH} (1.0) (units are mtus; 1mtu=48.9 fs) -- constant of the coupling to the thermal bath
1579 used with the Berendsen thermostat.
1581 \item{NOSEPOINCARE99} -- the Nose-Poincare thermostat as of 1999 will be used.
1583 \item{NOSEPOINCARE01} -- the Nose-Poincare thermostat as of 2001 will be used.
1585 \item{NOSEHOOVER96} -- the Nose-Hoover thermostat will be used.
1587 \item{Q\_NP=number} (real) (0.1) -- the value of the mass of the fictitious particle in the calculations
1588 with the Nose-Poincare thermostat.
1590 \item{T\_BATH} (300.0) (in K) -- temperature of canonical simulation or temperature to generate
1593 \item{ETAWAT} (0.8904) -- viscosity of water (in centipoises).
1595 \item{RWAT} (1.4) -- radius of water molecule (in A)
1597 \item{SCAL\_FRIC=number} (real) (0.02) -- scaling factor of the friction coefficients.
1599 \item{SURFAREA} -- scale friction acting on atoms by atoms' solvent accessible area.
1601 \item{RESET\_FRICMAT=number} (integer) (1000) -- recalculate friction matrix every RESET\_FRICMAT MD steps.
1603 \item{USAMPL} -- restraints on q (see reference 5 for meaning) will be imposed (see section .
1604 In this case, the next records specify the restraints; these records are
1605 placed before the list of temperatures or numbers of trajectories.
1607 \item{EQ\_TIME=number} (real) (1.0e4) -- time (in mtus; 1 mtu=48.9 fs) after which restraints
1608 on q will start to be in force.
1612 If USAMPL has been specified, the following information must be supplied after the
1613 main MD input data record (subroutine READ\_FRAGMENTS):
1615 Line 1: nset, npair, nfrag\_back (number of sets of restraints, number of restrained
1616 fragments, number of restrained pairs, number of restrained backbone fragments
1617 (in terms of $\theta$ and $\gamma$ angles)
1619 For each set of restraints (1, 2,..., nset):
1623 \item{mset(iset)} -- how many times the set is multiplied.
1625 \item{wfrag(i,iset), ifrag(1,i,iset), ifrag2(2,i,iset),qfrag(i,iset)} --
1626 weight of the restraint, first and last residue of the fragment, target q value.
1627 This information is repeated through nfrag.
1629 \item{wpair(i,iset), ipair(1,i,iset), ipair(2,i,iset),qinpair(i,iset)} --
1630 weight of the restraint, first and second fragment of the pair (according to fragment
1631 list), target q value. This information is repeated through npair
1633 \item{wfrag\_back(1,i,iset), wfrag\_back(2,i,iset), wfrag\_back(3,i,iset),
1634 ifrag\_back(1,i,iset),ifrag\_back(2,i,iset)} --
1635 weight of the restraints on $\theta$ angles, weight on the restraints on $\gamma$ angles,
1636 weight of the restraints on side-chain rotamers, first residue of the fragment,
1637 last residue of the fragment. This information is repeated through nfrag\_back.
1641 \subsubsection{REMD/MREMD data}
1642 label{sect:input:main:MREMD}
1644 (Miced format; subroutine READ\_REMDPAR.)
1648 \item{NREP} (3) -- number of replicas in a REMD/MREMD run.
1650 \item{NSTEX} (1000) -- number of steps after which exchange is performed in REMD/MREMD
1653 The temperatures in replicas can be specified through
1655 \item{RETMIN} (10.0) -- minimum temperature in a REMD/MREMD run,
1657 \item{RETMAX} (1000.0) -- maximum temperature in a REMD/MREMD run.
1661 Then the range from retmin to retmax is divided into equal segments and
1662 temperature of the replicas assigned accordingly,
1668 \item{TLIST} means that the NREP temperature of the replicas will be input in the
1671 \item{MLIST} numbers of trajectories per each of the NREP temperatures will be
1672 specified in the record after the list of temperatures; this specifies
1677 Important! The number of processors must be exactly equal to the number of
1678 trajectories, i.e., NREP for a REMD run or $\sum_i mlist(i)$ for a MREMD run.
1682 \item{SYNC} -- all trajectories will be synchronized every NSTEX time steps
1683 (by default, they are not synchronized).
1685 \item{TRAJ1FILE} -- only the master processor outputs coordinates. This feature pertains
1686 only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
1689 \item{REST1FILE} -- only the master writes the restart file.
1691 \item{HREMD} -- Hamiltonian replica exchange flag; not only temperatures but also
1692 sets energy-term weights are exchanged between conformations.
1694 \item{TONLY} -- run a ``fake'' HREMD with many sets of energy-term weights in a
1695 single run but only temperature exchange.
1699 \subsubsection{Energy-term and restraint weights}
1700 \label{sect:input:main:weights}
1702 (Data list format; subroutine MOLREAD.)
1706 \item{WLONG=number} (real) (1.0d0) --
1707 common weight of the U(SC-SC) (side-chain side-chain interaction)
1708 and U(SC,p) (side-chain peptide-group) term.
1710 \item{WSCC=number} (real) (WLONG) --
1711 weight of the U(SC-SC) term.
1713 \item{WSCP=number} (real) (WLONG)
1714 weight of the U(SC-p) term.
1716 \item{WELEC=number} (real) (1.0d0)
1717 weight of the U(p-p) (peptide-group peptide-group interaction) term.
1719 \item{WEL\_LOC=number} (real) (1.0d0)
1720 weight of the $U_{el;loc}^3$ (local-electrostatic cooperativity, third-order) term.
1722 \item{WCORRH=number} (real) (1.0d0)
1723 weight of the U(corr) (cooperativity of hydrogen-bonding interactions, fourth-order) term.
1725 \item{WCORR5=number} (real) (0.0d0) --
1726 weight of the $U_{el;loc}^5$ (local-electrostatic cooperativity, 5th order
1729 \item{WCORR6=number} (real) (0.0d0) --
1730 weight of the $U_{el;loc}^6$ (local-electrostatic cooperativity, 6th order
1733 \item{WTURN3=number} (real) (1.0d0) --
1734 weight of the $U_{turn}^3$ (local-electrostatic cooperativity within 3 residue
1735 segment, 3rd order contribution).
1737 \item{WTURN4=number} (real) (1.0d0) --
1738 weight of the $U_{turn}^4$ (local-electrostatic cooperativity within 4 residue
1739 segment, 4rd order contributions).
1741 \item{WTURN6=number} (real) (1.0d0) --
1742 weight of the $U_{turn}^6$ (local-electrostatic cooperativity within 6 residue
1743 segment, 6rd order contributions).
1745 \item{WTOR=number} (real) (1.0d0) --
1746 weight of the torsional term, $U_{tor}$.
1748 \item{WTORD=number} (real) (1.0d0) --
1749 weight of the double-torsional term, $U_{tord}$.
1751 \item{WSCCOR=number} (real) (1.0d0) --
1752 weight of the backbone-sidechain-torsional term, $U_{sccor}$.
1754 \item{WANG=number} (real) (1.0d0) --
1755 weight of the virtual-bond angle bending term, $U_b$.
1757 \item{WSCLOC=number} (real) (1.0d0) --
1758 weight of the side-chain rotamer term, $U_{SC}$.
1760 \item{WSTRAIN=number} (real) (1.0d0) --
1761 scaling factor of the distance-constrain or disulfide-bond strain energy term.
1763 \item{SCALSCP=number} (real) (1.0d0) --
1764 scaling factor of $U_{SCp}$; this is an alternative to specifying WSCP; in
1765 this case WSCP will be calculated as WLONG*SCALSCP.
1767 \item{SCAL14=number} (real) (1.0d0) --
1768 scaling factor of the 1,4 SC-p interactions.
1770 \item{CUTOFF} (7.0) -- cut-off on backbone-electrostatic interactions to compute 4-
1771 and higher-order correlations.
1773 \item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
1776 \item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
1780 The defaults are NOT the recommended values. No ``working'' default values
1781 have been set, because the force field is still under development. The values
1782 corresponding to the force fields listed in section 4 are as follows:
1786 WELEC=1.5 WSTRAIN=1.0 WTOR=0.08617 WANG=0.10384 WSCLOC=0.10384 WCORR=1.5 &
1787 WTURN3=0 WTURN4=0 WTURN6=0 WEL_LOC=0 WCORR5=0 WCORR6=0 SCAL14=0.40 SCALSCP=1.0 &
1788 CUTOFF=7.00000 WSCCOR=0.0
1793 WSC=1.00000 WSCP=0.72364 WELEC=1.10890 WANG=0.68702 WSCLOC=1.79888 &
1794 WTOR=0.30562 WCORRH=1.09616 WCORR5=0.17452 WCORR6=0.36878 WEL_LOC=0.19508 &
1795 WTURN3=0.00000 WTURN4=0.55588 WTURN6=0.11539 CUTOFF=7.00000 WCORR4=0.0000 &
1796 WTORD=0.0 WSCCOR=0.0
1801 WSC=1.00000 WSCP=1.10684 WELEC=0.70000 WANG=0.80775 WSCLOC=1.91939 &
1802 WTOR=3.36070 WCORRH=2.50000 WCORR5=0.99949 WCORR6=0.46247 WEL_LOC=2.50000 &
1803 WTURN3=1.80121 WTURN4=4.35377 WTURN6=0.10000 CUTOFF=7.00000 WCORR4=0.00000 &
1809 WSC=1.00000 WSCP=1.43178 WELEC=0.41501 WANG=0.37790 WSCLOC=0.12880 &
1810 WTOR=1.98784 WCORRH=2.50526 WCORR5=0.23873 WCORR6=0.76327 WEL_LOC=2.97687 &
1811 WTURN3=0.09261 WTURN4=0.79171 WTURN6=0.01074 CUTOFF=7.00000 WCORR4=0.00000 &
1817 WSC=1.00000 WSCP=1.54864 WELEC=0.20016 WANG=1.00572 WSCLOC=0.06764 &
1818 WTOR=1.70537 WTORD=1.24442 WCORRH=0.91583 WCORR5=0.00607 WCORR6=0.02316 &
1819 WEL_LOC=1.51083 WTURN3=2.00764 WTURN4=0.05345 WTURN6=0.05282 WSCCOR=0.0 &
1820 CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
1825 WSC=1.00000 WSCP=2.85111 WELEC=0.36281 WANG=3.95152 WSCLOC=0.15244 &
1826 WTOR=3.00008 WTORD=2.89863 WCORRH=1.91423 WCORR5=0.00000 WCORR6=0.00000 &
1827 WEL_LOC=1.72128 WTURN3=2.99827 WTURN4=0.59174 WTURN6=0.00000 &
1828 CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
1833 WSC=1.00000 WSCP=2.73684 WELEC=0.06833 WANG=4.15526 WSCLOC=0.16761 &
1834 WTOR=2.99546 WTORD=2.89720 WCORRH=1.98989 WCORR5=0.00000 WCORR6=0.00000 &
1835 WEL_LOC=1.60072 WTURN3=2.36351 WTURN4=1.34051 WTURN6=0.00000 &
1836 CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
1841 WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
1842 WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
1843 WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
1844 WVDWPP=0.11371 WHPB=1.00000 &
1845 CUTOFF=7.00000 WCORR4=0.00000
1850 WLONG=1.70905 WSCP=2.18310 WELEC=1.06684 WBOND=1.00000 WANG=1.17536 &
1851 WSCLOC=0.22070 WTOR=2.65798 WTORD=2.00646 WCORRH=0.23541 WCORR5=0.00000 &
1852 WCORR6=0.00000 WEL_LOC=0.42789 WTURN3=1.68126 WTURN4=0.75080 WTURN6=0.00000 &
1853 WVDWPP=0.27044 WHPB=1.00000 WSCP14=0.00000 &
1854 CUTOFF=7.00000 WCORR4=0.00000
1859 WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
1860 WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
1861 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
1862 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &
1863 CUTOFF=7.00000 WCORR4=0.00000
1866 \subsubsection{Input and/or reference PDB file name}
1867 \label{sect:input:main:PDB}
1869 (Text format; subroutine MOLREAD.)
1871 If PDBSTART or PDBREF was specified in the control card, this line contains
1872 the PDB file name. Trailing slashes to specify the full path are permitted.
1873 The file name can contain up to 64 characters.
1875 \subsubsection{Amino-acid sequence}
1876 \label{sect:input:main:sequence}
1880 This data appears, if PDBSTART was not specified, otherwise must not be present
1881 because the sequence would be taken from the PDB file. The first line contains
1882 the number of amino-acid residues, including the end groups (free format),
1883 the next lines contain the sequence in 20(1X,A3) format for the three-letter
1884 or 80A1 format for the one-letter code. There are two types of end-groups:
1885 Gly (three-letter code) or G (one-letter code), if an end group contains a full
1886 peptide bond (e.g., the acetyl N-terminal group or the carboxyamide C-terminal
1887 group) and D (in the three-letter code) or X (in the one-letter code), if the
1888 end group does not contain a peptide group (e.g., the NH2 N-terminal end group
1889 or the COOH C-terminal end group). (Note the Gly or G also denotes the regular
1890 glycine residue, if found in the middle of a chain).
1891 In the second case the end group is considered as a ``dummy'' group and serves
1892 only to define the first (last) virtual-bond dihedral angle $\gamma$ for the
1893 first (last) full amino-acid residue.
1895 Consider, for example, the Ac-Ala(19)-NHMe polypeptide. The three-letter code
1896 input will look like this:
1900 Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
1904 And the one-letter code input will be:
1908 GAAAAAAAAAAAAAAAAAAAG
1911 If the sequence is changed to NH3(+)-Ala(19)-COO(-), the inputs will look
1916 D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
1924 XAAAAAAAAAAAAAAAAAAAX
1927 The sequence input is case-insensitive, because the present version of UNRES
1928 considers each amino-acid residue as an L-residue (there are no torsional
1929 parameters for the combinations of the D- and L-residues yet). Furthermore,
1930 each peptide group is considered as a trans group.
1932 If the version of UNRES has multi-chain capacity, placing a dummy residue
1933 inside the sequence indicates start of a new chain. For example, a system
1934 composed of two Ala(10) chains can be specified as follows (3-letter code):
1938 D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D Ala Ala Ala Ala Ala Ala Ala Ala
1946 XAAAAAAAAAAXAAAAAAAAAAX
1949 \subsubsection{Disulfide-bridge information}
1950 \label{sect:input:main:disulphide}
1952 (Free format; subroutine READ\_BRIDGE.)
1960 \item{NS} -- the number of half-cystines (required even if no half-cystines are present).
1962 \item{ISS(i)} -- the position of ith half-cystine in the sequence (starting from the
1963 N-terminal end group)
1967 Next line(s) (present only, if $ns>0$ and must not appear otherwise):
1969 NSS,(IHPB(i),JHPB(i),i=1,NSS)
1973 \item{NSS} -- the number of disulfide bridges; must not be greater than NS/2.
1975 \item{IHPB(i),JHPB(i)} -- the cystine residue forming the ith bridge.
1979 The program will check, whether the residues specified in the ISS list
1980 are cystines and terminate with error, if any of them is not. The program
1981 also checks, if the numbers from the IHPB and the JHPB lists have appeared
1984 \subsubsection{Dihedral-angle restraint data}
1985 \label{sect:input:main:dihedral-restraints}
1987 (Free format; subroutine MOLREAD.)
1989 This set of data specifies the harmonic constraints (if any) imposed on selected
1990 virtual-bond dihedral angles $\gamma$.
1996 \item{NDIH\_CONSTR} -- the number of restrained $\gamma$ angles (required even if no
1997 restrains are applied).
2001 2nd line (present only, if NDIH\_CONSTR$>$0; must not appear otherwise):
2002 FTORS - the force constant expressed in kcal/(mol*rad**2)
2004 next NDIH\_CONSTR lines (present only, if NDIH\_CONSTR$>$0):
2006 IDIH\_CONSTR(i),PHI0(i),DRANGE(i)
2010 \item{IDIH\_CONSTR(i)} -- the number of ith restrained $\gamma$ angle. The angles are
2011 numbered after the LAST $\alpha$-carbons. Thus, the first ``real'' angle has number
2012 4 and it corresponds to the rotation about the CA(2)-CA(3) virtual-bond axis
2013 and the last angle has the number NRES and corresponds to the rotation about
2014 the CA(NRES-2)-CA(NRES-1) virtual-bond axis.
2016 \item{PHI0(i)} -- the ``center'' of the restraint (expressed in degrees).
2018 \item{DRANGE(i)} -- the ``flat well'' range of the restraint (in degrees).
2022 The restraint energy for the ith restrained angle is expressed as:
2025 E_{dih} = \begin{cases}
2026 \rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
2027 &<PHI0(i)+DRANGE(i)\\
2029 0 &\rm if\ \ PHI0(i)-DRANGE(i) \\
2030 &\le \gamma_{IDIH\_CONSTR(i)} \\
2031 &\le PHI0(i)+DRANGE(i)\\
2033 \rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
2038 Applying dihedral-angle constraints also implies that for ith constrained
2039 $\gamma$ angle the sampling be carried out from the
2040 [PHI0(i)-DRANGE(i)..PHI0(i)+DRANGE(i)] interval and not from the $[-\pi..\pi]$
2041 interval, if random conformations are generated. If only this and not
2042 restrained minimization is required, just set FTORS to 0.
2044 \subsubsection{Distance restraints}
2045 \label{sect:input:main:disance-restraints}
2047 (Mixed format; subroutine READ\_DIST\_CONSTR.)
2049 Restraints are imposed on C$^\alpha\cdots$C$^\alpha$ SC$\cdots$SC distances (C$^\beta\cdots$C$^\beta$.
2053 \item{NDIST=number} (integer) (0) -- number of restraints on specific distances.
2055 \item{NFRAG=number} (integer) (0) -- number of distance-restrained protein segments.
2057 \item{NPAIR=number} (integer) (0) -- number of distance-restrained pairs of segments.
2058 Specifying NPAIR requires specification of segments.
2060 \item{IFRAG=start(1),end(1),start(2),end(2)...start(NFRAG),end(NFRAG)} (integers) --
2061 First and last residues of the distance restrained segments.
2063 \item{WFRAG=w(1),w(2),...,w(NFRAG) (reals)} -- force constants or bases for force
2064 constant calculation corresponding to fragment restraints.
2066 \item{IPAIR=start(1),end(1),start(2),end(2),...,start(NPAIR),end(NPAIR)} (integers)
2067 -- numbers of segments (consecutive numbers of start or end pairs in IFRAG
2068 specification), the distances between which will be restrained.
2070 \item{WPAIR=w(1),w(2),...,w(NFRAG)} (reals) -- force constants or bases for force
2071 constant calculation corresponding to pair restraints.
2073 \item{DIST\_CUT=number} (real) (5.0) -- the cut-off distance in angstroms for force-
2074 constant calculations.
2076 The force constants within fragments/between pairs of fragments are calculated
2077 depending on the value of DIST\_CONSTR described in section 5.1:
2081 \item{1} -- all force constants are equal to the respective entries of WFRAG/WPAIR
2083 \item{2} -- the force constants are equal to the respective entries of WFRAG/WPAIR
2084 when the distance between the C$^\alpha$ atoms in the reference structure
2085 $\le$D\_CUT, 0 otherwise.
2087 \item{3} -- the force constants are calculated from the formula:
2091 \item{$k(C^\alpha_j,C^\alpha_k)=W\times\exp{-[d(C^\alpha_j,C^\alpha_k)/DIST\_CUT)]^2/2}$}
2093 where $k(C^\alpha_j,C^\alpha_k)$ is the force constant between the respective C$^\alpha$ atoms,
2094 $d(C^\alpha_j,C^\alpha_k)$ is the distance between these C$^\alpha$ atoms in the reference
2095 structure, and W is the basis for force-constant calculation (see above).
2099 The above restraints are harmonic resatraints of the form
2102 E_{dis} = \sum_i k_i \left(d_i - d_i^{ref}\right)^2
2105 where $d_i$ is the distance in the calculated structure and $d_i^{ref}$ is the respective
2106 distance in the reference (PDB) structure. The reference structure is required.
2108 If NDIST$>$0, the restraints on specific distance are input explicitly (no reference structure is requires).
2109 The restraints are quartic restraints of a similar form as that in section
2110 \ref{sect:input:main:dihedral-restraints} but with angles replaced with distances.
2112 ihpb(i), jhpb(i), dhpb(i), dhpb1(i), ibecarb(i), forcon(i), i=1,NDIST
2116 \item{ihpb(i)} and jhpb(i) are the numbers of the residues the distance
2117 between the C$^\alpha$ atoms of which will be distance restrained,
2119 \item{dhpb(i)} and dhpb1(i) are the lower and upper distance-restraint,
2121 \item{ibecarc(i)} is the restraint-type flag;
2122 ibecarb(i)==0 indicates that the restraints are imposed on the
2123 C$^\alpha\cdots$C$^\alpha$ distances; otherwise restraints on the
2124 SC$\cdots$SC distances are imposed,
2127 is the respective force constant.
2131 \subsubsection{Internal coordinates of the reference structure}
2132 \label{sect:input:main:internalref}
2134 (Free format; subroutine READ\_ANGLES.)
2136 This part of the data is present, if REFSTR, but not PDBREF was specified,
2137 otherwise must not appear. It contains the following group of variables:
2140 \item{(THETA(i),i=3,NRES)} -- the virtual-bond valence angles THETA.
2141 \item{(PHI(i),i=4,NRES)} -- the virtual-bond dihedral angles GAMMA.
2142 \item{(ALPH(i),i=2,NRES-1)} -- the ALPHA polar angles of consecutive side chains.
2143 \item{(OMEG(i),i=2,NRES-1)} -- the BETA polar angles of consecutive side chains.
2146 ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
2147 is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
2148 CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
2151 \subsubsection{Distance-distribution (SAXS-restraint) data}
2153 This section contains the probability distribution ($P(r)$) from SAXS
2154 measurements to be used as restraints through introduction of a maximum-likelihood term.
2155 Each entry is in a separate like and the number of entries must equal to
2156 NSAXS specified in the first data record. Each line contains the position
2157 of the left side of the distance bin and probability-distribution value, for
2161 0.7100E-00 0.2036E-03
2162 0.1420E+01 0.4221E-03
2165 The distance-distribution values do not need to be input in normalized form.
2166 Normalization is carried out automatically. It should be noted that neither
2167 probabilities nor distances can be zero; otherwise the calculations will crash.
2168 Therefore, entries with zeros must be eliminated from the data.
2170 \subsubsection{Internal coordinates of the initial conformation}
2171 \label{sect:input:main:intcoord}
2173 (Free format; subroutine READ\_ANGLES.)
2175 This part of the data is present, if RAND\_CONF, MULTCONF, THREAD, or PDBSTART
2176 were not specified, otherwise must not appear. This input is as in section \ref{sect:support}.
2178 \paragraph{File name with internal coordinates of the conformations to be processed}
2179 \label{sect:input:main:intcord:files}
2181 (Text format; subroutine MOLREAD.)
2183 This data is present only, if MULTCONF was specified. It contains the name of
2184 the file with the internal coordinates. Up to 64 characters are allowed.
2185 The structure of the file is that of the *.int file produced by UNRES/CSA.
2186 See section ``The structure of the INT files'' for details.
2188 \subsubsection{Control data for energy map construction}
2189 \label{sect:input:main:map}
2191 (Data list format; subroutine MAP\_READ.)
2193 These data lists appear, if NMAP=n was specified, where n is the number of
2194 variables that will be grid-searched. One list is per one variable or a
2195 group of variables set equal (see below):
2198 \item{PHI} -- the variable is a virtual-bond dihedral angle $\gamma$.
2199 \item{THE} -- the variable is a virtual-bond angle $\theta$.
2200 \item{ALP} -- the variable is a side-chain polar angle $\alpha$.
2201 \item{OME} -- the variable is a side-chain polar angle $\beta$.
2205 \item{RES1=number} (integer)
2206 \item{RES2=number} (integer)
2209 The range of residues for which the values will be set; all these variables
2210 will be set at the same value. It is required that RES2$>$RES1.
2213 \item{FROM=angle} (real)
2214 \item{TO=angle} (real)
2217 Lower and upper limit of scanning in grid search (in degrees)
2220 \item{NSTEP=number} (integer)
2223 Number of steps in scanning along this variable/group of variables.
2225 \subsection{Input coordinate files}
2226 \label{sect:input:coordfiles}
2228 (Text format; subroutine MOLREAD.)
2230 At present, geometry can be input either from the external files in the PDB
2231 format (with the PDBSTART option) or multiple conformations can be read
2232 as virtual-bond-valence and virtual-bond dihedral angles when the MULTCONF
2233 option is used (the latter, however, implies using standard virtual-bond
2234 lengths as initial values). The structure of internal-coordinate files
2235 is the same as that of output internal-coordinate files described in section
2238 \subsection{Other input files}
2239 \label{sect:input:otherfiles}
2241 CSA parameters can optionally be read in free format from file INPUT.CSA.in
2242 (see section 8.1.4). When a CSA run is restarted, the CSA-specific output files
2243 also serve as input files. INPUT is the prefix of input and output files
2244 as explained in section \ref{sect:command}.
2246 Restart files for MD and REMD simulations. They are read when the keyword
2247 RESTART appears on the MD/REMD data group (section \ref{sect:input:main:MD}).
2251 \section{OUTPUT FILES}
2254 UNRES ``main'' output files (INPUT.out\_\$\{POT\}[processor]) are log files from
2255 a run. They contain the information of the molecule, force field, calculation
2256 type, control parameters, etc.; however, not the structures produced during
2257 the run or their energies except single-point energy evaluation and
2258 minimization-related runs. The structural information is included in
2259 coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat),
2260 respectively; these files are further processed by other programs (WHAM,
2261 CLUSTER) or can be viewed by molecular viewers (pdb or mol2 files).
2263 \subsection{Coordinate files}
2264 \label{sect:output:coord}
2266 \subsubsection{The internal coordinate (INT) file}
2267 \label{sect:output:coord:int}
2269 This file contains the internal coordinates of the conformations produced
2270 by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so
2271 only the angular variables are provided.
2273 IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)\\
2274 (I5,F12.5,I2,9(1X,2I3))
2277 \item{IT} -- the number of the conformation.
2278 \item{ENER} -- total energy.
2279 \item{NSS} -- the number of disulfide bridges.
2280 \item{(IHPB(I),JHPB(I),I=1,NSS)} -- the positions of the pairs of half-cystines .
2281 forming the bridges. If NSS$>9$9, the remaining pairs are written in the
2282 following lines in the (3X,11(1X,2I3)) format.
2285 (THETA(I),I=3,NRES)\\
2288 The virtual-bond angles THETA (in degrees)
2293 The virtual-bond dihedral angles GAMMA (in degrees)
2295 (ALPH(I),I=2,NRES-1)\\
2296 (OMEG(I),I=2,NRES-1)\\
2299 The polar angles ALPHA and BETA of the side-chain centers (in degrees).
2301 \subsubsection{The plain Cartesian coordinate (X) files}
2302 \label{sect:output:coord:cart}
2304 (Subroutine CARTOUT.)
2306 This file contains the Cartesian coordinates of the $\alpha$-carbon and
2307 side-chain-center coordinates. All conformations from an MD/MREMD
2308 trajectory are collated to a single file. The structure of each
2309 conformation's record is as follows:
2311 1st line: time, potE, uconst, t\_bath,nss, (ihpb(j), jhpb(j), j=1,nss),
2312 nrestr, (qfrag(i), i=1,nfrag), (qpair(i), i=1,npair),
2313 (utheta(i), ugamma(i), uscdiff(i), i=1,nfrag\_back)
2316 \item{time:} MD time (in ``molecular time units'' 1 mtu = 4.89 fs),
2317 \item{potE:} potential energy,
2318 \item{uconst:} restraint energy corresponding to restraints on Q and backbone geometry,
2319 (see section \ref{sect:input:main:MD}),
2320 \item{t\_bath:} thermostat temperature,
2321 \item{nss:} number of disulfide bonds,
2322 \item{ihpb(j), jhpb(j):} the numbers of linked cystines for jth disulfide bond,
2323 \item{nrestr:} number of restraints on q and local geometry,
2324 \item{qfrag(i):} q value for ith fragment,
2325 \item{qpair(i):} q value for ith pair,
2326 \item{utheta(i):} sum of squares of the differences between the theta angles
2327 of the current conformation from those of the experimental conformation,
2328 \item{ugamma(i):} sum of squares of the differences beaten the gamma angles
2329 of the current conformation from those of the experimental conformation,
2330 \item{uscdiff(i):} sum of squares of the differences between the Cartesian difference
2331 of the unit vector of the C$^\alpha$-SC axis of the current conformation from
2332 those of the experimental conformation.
2335 Next lines: Cartesian coordinates of the C$^\alpha$ atoms (including dummy atoms)
2336 (sequentially, 10 coordinates per line)
2337 Next lines: Cartesian coordinates of the SC atoms (including glycines and
2338 dummy atoms) (sequentially, 10 coordinates per line)
2340 \subsubsection{The compressed Cartesian coordinate (CX) files}
2341 \label{sect:output:coord:cx}
2343 These files are compressed binary files (extension cx). For each conformation,
2344 the items are written in the same order as specified in section \ref{sect:output:coord:cx}. For
2345 MREMD runs, if TRAJ1FILE is specified on MREMD record (see section \ref{sect:input:main:MD}),
2346 snapshots from all trajectories are written every time the coordinates
2347 are dumped. Thus, the file contains snapshot 1 from trajectory 1, ...,
2348 snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.
2350 The compressed cx files can be converted to pdb file by using the xdrf2pdb
2351 auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple
2352 trajectory files from MREMD runs generated by using the TRAJ1FILE option).
2353 The multiple-trajectory cx files are also input files for the auxiliary
2356 \subsubsection{The Brookhaven Protein Data Bank format (PDB) files}
2357 \label{sect:output:coord:PDB}
2359 (Subroutine PDBOUT.)
2362 These files are written in PDB standard (see. e.g.,
2363 \href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{\textcolor{blue}{ftp://ftp.wwpdb.org/pub/pdb\-/doc/\-format\_descriptions}}). %\-/Format\_v33\_Letter.pdf}.
2364 The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
2365 The C$^\alpha$ (marked CA) and SC (marked CB) coordinates are output. The CONECT
2366 records specify the C$^\alpha\cdots$C$^\alpha$ and C$^\alpha\cdots$SC virtual bonds. Secondary
2367 structure is detected based on peptide-group contacts, as specified in
2368 ref 12. Dummy residues are omitted from the output. If the program has
2369 multiple-chain function, the presence of a dummy residue in a sequence
2370 starts a new chain, which is assigned the next alphabet letter as ID, and
2371 residue numbering is started over.
2373 \subsubsection{The SYBYLL (MOL2) files}
2374 \label{sect:output:coord:subyll}
2376 See the description of mol2 format (e.g.,
2377 \href{http://tripos.com/data/support/mol2.pdf}{http://tripos.com/data/support/mol2.pdf}.
2378 Similar remarks apply as for
2379 the PDB format (section \ref{sect:output:coord:PDB}).
2381 \subsection{The summary (STAT) file}
2383 \subsubsection{Non-MD runs}
2385 This file contains a short summary of the quantities characterizing the
2386 conformations produced by UNRES/CSA. It is created for MULTCONF and MCM.
2388 NOUT,EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS,ETOT,RMS,FRAC\\
2392 \item{NOUT} -- the number of the conformations
2393 \item{EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS} -- energy components
2394 \item{ETOT} -- total energy
2395 \item{RMS} -- RMS deviation from the reference structure (if REFSTR was specified)
2396 \item{FRAC} -- fraction of side chain - side chain contacts of the reference
2397 structure present in this conformation (if REFSTR was specified)
2400 \subsubsection{MD and MREMD runs}
2401 \label{sect:output:coord:MD}
2403 Each line of the stat file generated by MD/MREMD runs contains the following
2407 \item{step} -- the number of the MD step
2408 \item{time} -- time [unit is MTU (molecular time unit) equal to 48.9 fs]
2409 \item{Ekin} -- kinetic energy [kcal/mol]
2410 \item{Epot} -- potential energy [kcal/mol]
2411 \item{Etot} -- total energy (Ekin+Epot)
2412 \item{H-H0} -- the difference between the cureent and initial extended Hamiltionian
2413 in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
2414 \item{RMSD} -- root mean square deviation from the reference structure (only in
2415 REFSTR has been specified)
2416 item{damax} -- maximum change of acceleration between two MD steps
2417 \item{fracn} -- fraction of native side-chain concacts (very crude, based on
2418 SC-SC distance only)
2419 \item{fracnn} -- fraction of non-native side-chain contacts
2420 \item{co} -- contact order
2421 \item{temp} -- actual temperature [K]
2422 \item{T0} -- initial (microcanonical runs) or thermostat (other run types)
2424 \item{Rgyr} -- radius of gyration based on C$^\alpha$ coordinates [A]
2425 \item{proc} -- in MREMD runs the number of the processor (the number of the
2426 trajectory less 1); not present for other runs.
2429 For an USAMPL run, the following items follow the above list:
2432 \item{iset} -- the number of the restraint set
2433 \item{uconst} -- restraint energy pertaining to q-values
2434 \item{uconst\_back} -- restraint energy pertaining to virtual-backbone restraints
2435 \item{(qfrag(i),i=1,nfrag)} -- q values of the specified fragments
2436 \item{(qpair(ii2),ii2=1,npair)} -- q values of the specified pairs of fragments
2437 \item{(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag\_back)} -- virtual-backbone and
2438 side-chain-rotamer restraint energies of the fragments specified
2441 If PRINT\_COMPON has been specified, the energy components are printed
2442 after the items described above.
2444 \subsection{CSA-specific output files}
2445 \label{sect:output:coord:CSA}
2447 There are several output files from the CSA routine:
2448 INPUT.CSA.seed, INPUT.CSA.history, INPUT.CSA.bank, INPUT.CSA.bank1,
2449 INPUT.CSA.rbank INPUT.CSA.alpha, INPUT.CSA.alpha1.
2451 The most informative outfile is INPUT.CSA.history. This file first write down
2452 the parameters in INPUT.CSA.csa file. Later it shows the energies of random
2453 minimized conformations in its generation. After sorting the First\_bank
2454 in energy (ascending order), the energies of the First\_bank is re-written here.
2455 After this the output looks like:
2458 1 0 100 6048.2 1 100-224.124-114.346 202607 100 100
2459 1 0 700 5882.6 2 29-235.019-203.556 1130308 100 100
2460 1 0 1300 5721.5 2 18-242.245-212.138 2028008 100 100
2461 1 0 1900 5564.8 13 54-245.185-218.087 2897988 98 100
2462 1 0 2500 5412.4 13 61-246.214-222.068 3706478 97 100
2463 1 0 3100 5264.2 13 89-248.715-224.939 4514196 96 100
2466 Each line is written between each iteration (just after selection
2467 of seed conformations) containing following data:
2468 jlee,icycle,nstep,cutdif,ibmin,ibmax,ebmin,ebmax,nft,iuse,nbank
2469 ibmin and ibmax lists the index of bank conformations corresponding to the
2470 lowest and highest energies with ebmin and ebmax.
2471 nft is the total number of function evaluations so far.
2472 iuse is the total number of conformations which have not been used as seeds
2473 prior to calling subroutine select\_is which select seeds.
2475 Therefore, in the example shown above, one notes that so far 3100
2476 minimizations has been performed corresponding to the total of 4514196
2477 function evaluations. The lowest and highest energy in the Bank is
2478 -248.715 (\#13) and -224.939 (\#89), respectively. The number of conformations
2479 already used as seeds (not including those selected as seeds in this iteration)
2480 so far is 4 (100-96).
2482 The files INPUT.CSA.bank and INPUT.CSA.rbank contains data of Bank and
2483 First\_bank. For more information on these look subroutines write\_bank
2484 and write\_rbank. The file INPUT.CSA.bank is overwritten between each
2485 iteration whereas Bank is accumulated in INPUT.CSA.bank1 (not for every
2486 iteration but as specified in the subroutine together.f).
2488 The file INPUT.CSA.seed lists the index of the seed conformations with their
2489 energies. Files INPUT.CSA.alpha, INPUT.CSA.alpha1 are written only once
2490 at the beginning of the CSA run. These files contain some arrays used
2495 \section{TECHNICAL SUPPORT CONTACT INFORMATION}
2496 \label{sect:support}
2499 Faculty of Chemistry, University of Gdansk\\
2500 ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
2501 phone: +48 58 523 5124\\
2502 fax: +48 58 523 5012\\
2503 e-mail: \href{mailto:adam@sun1.chem.univ.gda.pl}{adam@sun1.chem.univ.gda.pl}\\
2505 Dr. Cezary Czaplewski\\
2506 Faculty of Chemistry, University of Gdansk\\
2507 ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
2508 phone: +48 58 523 5126\\
2509 fax: +48 58 523 5012\\
2510 e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}\\
2512 Dr. Adam Sieradzan\\
2513 Faculty of Chemistry, University of Gdansk\\
2514 ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
2515 phone: +48 58 523 5124\\
2516 fax: +48 58 523 5012\\
2517 e-mail: \href{mailto:adasko@sun1.chem.univ.gda.pl}{adasko@sun1.chem.univ.gda.pl}\\
2519 Dr. Stanislaw Oldziej\\
2520 Intercollegiate Faculty of Biotechnology\\
2521 University of Gdansk, Medical University of Gdansk\\
2522 ul. Kladki 22, 80-922 Gdansk, Poland\\
2523 phone: +48 58 523 5361\\
2524 fax: +48 58 523 5472\\
2525 e-mail: \href{mailto:stan@biotech.ug.edu.pl}{stan@biotech.ug.edu.pl}\\
2528 Korea Institute for Advanced Study\\
2529 207-43 Cheongnyangni 2-dong, Dongdaemun-gu,\\
2530 Seoul 130-722, Korea\\
2531 phone: +82-2-958-3890\\
2532 fax: +82-2-958-3731\\
2533 email: \href={mailto:jlee@kias.re.kr}{jlee@kias.re.kr}
2536 Prepared by Adam Liwo and Jooyoung Lee, 7/17/99\\
2537 Revised by Cezary Czaplewski 1/4/01\\
2538 Revised by Cezary Czaplewski and Adam Liwo 8/26/03\\
2539 Revised by Cezary Czaplewski and Adam Liwo 11/26/11\\
2540 Revised by Adam Liwo 02/19/12\\
2541 LaTeX version by Adam Liwo 09/25/12\\
2542 revised by Adam Liwo 12/04/14