--- /dev/null
+ UNRES - A PROGRAM FOR COARSE-GRAINED SIMULATIONS OF PROTEINS
+ ------------------------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. Credits
+
+3. General information
+ 3.1. Purpose
+ 3.2. Functions of the program
+ 3.2. Companion programs
+ 3.4. Programming language
+ 3.5. References
+
+4. Installation
+
+5. Customizing your batch and C-shell script
+
+6. Command line and files
+
+7. Force fields
+
+8. Input files
+ 8.1. Main input data file
+ 8.1.1. Title
+ 8.1.2. Control data (data list format; READ_CONTROL subroutine)
+ 8.1.2.1 Keywords to chose calculation type
+ 8.1.2.2 Specification of protein and structure output in non-MD
+ applications
+ 8.1.2.3. Miscellaneous
+ 8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+ 8.1.4. CSA control parameters
+ 8.1.5. MCM data (data list, subroutine MCMREAD)
+ 8.1.6. MD data (subroutine READ_MDPAR)
+ 8.1.7. REMD/MREMD data (subroutine READ_REMDPAR)
+ 8.1.8. Energy-term weights (data list; subroutine MOLREAD)
+ 8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+ 8.1.10. Amino-acid sequence (free and text format)
+ 8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+ 8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+ 8.1.13. Distance restraints (subroutine READ_DIST_CONSTR)
+ 8.1.14. Internal coordinates of the reference structure (free format;
+ subroutine READ_ANGLES)
+ 8.1.15. Internal coordinates of the initial conformation (free format;
+ subroutine READ_ANGLES)
+ 8.1.15.1. File name with internal coordinates of the conformations
+ to be processed
+ 8.1.16 Control data for energy map construction (data lists;
+ subroutine MAP_READ)
+ 8.2. Parameter files
+ 8.3. Input coordinate files
+ 8.4. Other input files
+
+9. Output files
+ 9.1. Coordinate files
+ 9.1.1. The internal coordinate (INT) files
+ 9.1.2. The plain Cartesian coordinate (X) files
+ 9.1.3. The compressed Cartesian coordinate (CX) files
+ 9.1.4. The Brookhaven Protein Data Bank format (PDB) files
+ 9.1.5. The SYBYLL (MOL2) files
+ 9.2. The summary (STAT) file
+ 9.2.1. Non-MD runs
+ 8.2.2. MD and MREMD runs
+ 9.3. CSA-specific output files
+
+10. Technical support contact information
+
+1. LICENSE TERMS
+----------------
+
+* 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.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* 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.
+
+2. CREDITS
+----------
+
+The current and former developers of UNRES are listed in this section in alphabetic
+order together with their current or former affiliations.
+
+Maurizio Chinchio (formerly Cornell Univ., USA)
+Cezary Czaplewski (Univ. of Gdansk, Poland)
+Carlo Guardiani (Georgia State Univ., USA)
+Yi He (Cornell Univ., USA)
+Justyna Iwaszkiewicz (Swiss Institute of Bioinformatics, Switzerland)
+Dawid Jagiela (Univ. of Gdansk, Poland)
+Stanislaw Jaworski (deceased)
+Sebastian Kalinowski (Univ. of Gdansk, Poland)
+Urszula Kozlowska (deceased)
+Rajmund Kazmierkiewicz (Univ. of Gdansk, Poland)
+Jooyoung Lee (Korea Institute for Advanced Studies, Korea)
+Adam Liwo (Univ. of Gdansk, Poland)
+Mariusz Makowski (Univ. of Gdansk, Poland)
+Marian Nanias (formerly Cornell Univ., USA)
+Stanislaw Oldziej (Univ. of Gdansk, Poland)
+Jaroslaw Pillardy (Cornell Univ., USA)
+Daniel Ripoll (formerly Cornell Univ., USA)
+Jeff Saunders (Schrodinger Inc., USA)
+Harold A. Scheraga (Cornell Univ., USA)
+Hujun Shen (Dalian Institute of Chemical Physics, P.R. China)
+Adam Sieradzan (Univ. of Gdansk, Poland)
+Ryszard Wawak (formerly Cornell Univ., USA)
+Bartlomiej Zaborowski (Univ. of Gdansk, Poland)
+
+3. GENERAL INFORMATION
+----------------------
+
+3.1. Purpose
+------------
+
+Run coarse-grained calculations of polypeptide chains with the UNRES force field.
+There are two versions of the package which should be kept separate because of
+non-overlapping functions: version which runs global optimization (Conformational
+Space Annealing, CSA) and version that runs coarse-grained molecular dynamics and
+its extension. Because the installation, input file preparation and running CSA
+and MD versions are similar, a common manual is provided. Items specific
+for the CSA and MD version are marked "CSA" and "MD", respectively.
+
+MD version can be used to run multiple-chain proteins (however, that version of
+the code is a new release and might fail if yet un-checked functions are used).
+The multi-chain CSA version for this purpose is another package (written largely in
+C++).
+
+3.2. Functions of the program
+-----------------------------
+
+1. Perform energy evaluation of a single or multiple conformations
+ (serial and parallel) (CSA and MD)
+
+2. Run canonical mesoscopic molecular dynamics (serial and parallel) (MD).
+
+3. Run replica exchange (REMD) and multiplexing replica exchange (MREMD)
+ dynamics (parallel only) (MD).
+
+4. Run multicanonical molecular dynamics (parallel only) (MD).
+
+5. Run energy minimization (serial and parallel) (CSA and MD).
+
+6. Run conformational space annealing (CSA search) (parallel only) (CSA).
+
+7. Run Monte Carlo plus Minimization (MCM) (parallel only) (CSA).
+
+8. Run conformational family Monte Carlo (CFMC) calculations (CSA).
+
+9. Thread the sequence against a database from the PDB and minimize energy of
+ each structure (CSA).
+
+Energy and force evaluation is parallelized in MD version.
+
+3.3. Companion programs
+-----------------------
+
+The structures produced by UNRES can be used as inputs to the following programs provided
+with this package or separately:
+
+xdrf2pdb - converts the compressed coordinate files from MD (but not MREMD)runs into
+ PDB format.
+
+xdrf2pdb-m - same for MREMD runs (multiple trajectory capacity).
+
+xdrf2x - converts the plain Cartesian coordinate files into PDB format.
+
+WHAM - processes the coordinate files from MREMD runs and computes temperature profiles
+ of ensemble averages and computes the probabilities of conformations at selected
+ temperatures; also prepares data for CLUSTER and ZSCORE.
+
+CLUSTER - does the cluster analysis of the conformations; for MREMD runs takes the
+ coordinate files from WHAM which contain information to compute probabilities
+ of conformations at any temperature.
+
+PHOENIX - conversion of UNRES conformations to all-atom conformations.
+
+ZSCORE - force field optimization (for developers).
+
+Please consult the manuals of the corresponding packages for details. Note that not
+all of these packages are released yet; they will be released depending on their
+readiness for distribution. Contact Adam Liwo, Cezary Czaplewski or Stanislaw Oldziej
+for developmental versions of these programs.
+
+3.4. Programming language
+-------------------------
+
+This version of UNRES is written almost exclusively in Fortran 77; some subroutines
+for data management are in ansi-C. The package was parallelized with MPI.
+
+3.5. References
+---------------
+
+Citing the following references in your work that makes use of UNRES is gratefully
+acknowledged:
+
+[1] A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ I: Functional forms and parameters of long-range side-chain interaction potentials
+ from protein crystal data. J. Comput. Chem., 1997, 18, 849-873.
+
+[2] A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ II: Parameterization of local interactions and determination
+ of the weights of energy terms by Z-score optimization.
+ J. Comput. Chem., 1997, 18, 874-887.
+
+[3] A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Oldziej, R.J. Wawak,
+ S. Rackovsky, M.R. Pincus, H.A. Scheraga.
+ United-residue force field for off-lattice protein-structure simulations.
+ III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
+ J. Comput. Chem., 1998, 19, 259-276.
+
+[4] A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Cumulant-based expressions for the multibody terms for the correlation between
+ local and electrostatic interactions in the united-residue force field.
+ J. Chem. Phys., 2001, 115, 2323-2347.
+
+[5] J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, H.A. Scheraga,
+ Optimization of parameters in macromolecular potential energy functions by
+ conformational space annealing. J. Phys. Chem. B, 2001, 105, 7291-7298
+
+[6] J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll,
+ P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga,
+ Development of physics-based energy functions that predict medium-resolution
+ structures for proteins of the alpha, beta, and alpha/beta structural classes.
+ J. Phys. Chem. B, 2001, 105, 7299-7311
+
+[7] A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H.A. Scheraga.
+ A method for optimizing potential-energy functions by a hierarchical design
+ of the potential-energy landscape: Application to the UNRES force field.
+ Proc. Natl. Acad. Sci. U.S.A., 2002, 99, 1937-1942.
+
+[8] J. A. Saunders and H.A. Scheraga.
+ Ab initio structure prediction of two $\alpha$-helical oligomers
+ with a multiple-chain united-residue force field and global search.
+ Biopolymers, 2003, 68, 300-317.
+
+[9] J.A. Saunders and H.A. Scheraga.
+ Challenges in structure prediction of oligomeric proteins at the united-residue
+ level: searching the multiple-chain energy landscape with CSA and CFMC procedures.
+ Biopolymers, 2003, 68, 318-332.
+
+[10] S. Oldziej, U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of the potentials of mean force for rotation about Calpha-Calpha
+ virtual bonds in polypeptides from the ab initio energy surfaces of terminally
+ blocked glycine, alanine, and proline. J. Phys. Chem. A, 2003, 107, 8035-8046.
+
+[11] A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga.
+ Parameterization of backbone-electrostatic and multibody contributions
+ to the UNRES force field for protein-structure prediction from ab initio
+ energy surfaces of model systems. J. Phys. A, 2004, 108, 9421-9438.
+
+[12] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+[13] S. Oldziej, J. Lagiewka, A. Liwo, C. Czaplewski, M. Chinchio,
+ M. Nanias, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 3. Use of many proteins in optimization.
+ J. Phys. Chem. B., 2004, 108, 16950-16959.
+
+[14] M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ I. Lagrange equations of motion and tests of numerical stability in the
+ microcanonical mode, J. Phys. Chem. B, 2005, 109, 13785-13797.
+
+[15] M. Khalili, A. Liwo, A. Jagielska, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ II. Langevin and Berendsen-bath dynamics and tests on model $\alpha$-helical
+ systems. J. Phys. Chem. B, 2005, 109, 13798-13810.
+
+[16] A. Liwo, M. Khalili, H.A. Scheraga.
+ Ab initio simulations of protein-folding pathways by molecular dynamics with
+ the united-residue model of polypeptide chains.
+ Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 2362-2367.
+
+[17] F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga.
+ Implementation of a symplectic multiple-time-step molecular dynamics algorithm,
+ based on the united-residue mesoscopic potential energy function.
+ J. Chem. Phys., 2006, 125, 204107.
+
+[18] M. Nanias, C. Czaplewski, H.A. Scheraga.
+ Replica exchange and multicanonical algorithms with the coarse-grained
+ united-residue (UNRES) force field.
+ J. Chem. Theory and Comput., 2006, 2, 513-528.
+
+[19] A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+ H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential energy
+ function for canonical simulations. I. Temperature dependence of the effective
+ energy function and tests of the optimization method with single training
+ proteins.
+ J. Phys. Chem. B, 2007, 111, 260-285.
+
+[20] U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of virtual-bond-angle potentials of mean force for coarse-grained
+ simulations of protein structure and folding from ab initio energy surfaces of
+ terminally-blocked glycine, alanine, and proline.
+ J. Phys.: Condens. Matter, 2007, 19, 285203.
+
+[21] M. Chinchio, C. Czaplewski, A. Liwo, S. Oldziej, H.A. Scheraga.
+ Dynamic formation and breaking of disulfide bonds in molecular dynamics
+ simulations with the UNRES force field.
+ J. Chem. Theory and Comput., 2007, 3, 1236-1248.
+
+[22] A.V. Rojas, A. Liwo, H.A. Scheraga.
+ Molecular dynamics with the united-residue force field: Ab Initio folding
+ simulations of multichain proteins.
+ J. Phys. Chem. B, 2007, 111, 293-309.
+
+[23] A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz,
+ M. Makowski, R.K. Murarka, H.A. Scheraga.
+ Simulation of protein structure and dynamics with the coarse-grained UNRES
+ force field. In: Coarse-Graining of Condensed Phase and Biomolecular
+ Systems., ed. G. Voth, Taylor & Francis, 2008, Chapter 8, pp. 107-122.
+
+[24] C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga.
+ Application of multiplexed replica exchange molecular dynamics
+ to the UNRES force field: tests with $\alpha$ and $\alpha+\beta$ proteins.
+ J. Chem. Theor. Comput., 2009, 5, 627-640.
+
+[24] Y. He, Y. Xiao, A. Liwo, H.A. Scheraga.
+ Exploring the parameter space of the coarse-grained UNRES force field by random
+ search: selecting a transferable medium-resolution force field.
+ J. Comput. Chem., 2009, 30, 2127-2135.
+
+[25] U. Kozlowska, A. Liwo. H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 1. The Method.
+ J. Comput. Chem., 2010, 31, 1143-1153.
+
+[26] U. Kozlowska, G.G. Maisuradze, A. Liwo, H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 2. Results, comparison with statistical
+ potentials, and implementation in the UNRES force field.
+ J. Comput. Chem., 2010, 31, 1154-1167.
+
+[27] A. Liwo, S. Oldziej, C. Czaplewski, D.S. Kleinerman, P. Blood, H.A. Scheraga.
+ Implementation of molecular dynamics and its extensions with the coarse-grained
+ UNRES force field on massively parallel systems; towards millisecond-scale
+ simulations of protein structure, dynamics, and thermodynamics.
+ J. Chem. Theor. Comput., 2010, 6, 890-909.
+
+4. INSTALLATION
+---------------
+
+The distribution is contained in the UNRES.tar.gz file. To uncompress say:
+
+gzip -cd UNRES.tar.gz | tar xf -
+
+This will produce a directory named UNRES with the following subdirectories:
+
+src_CSA - the CSA-version source directory.
+
+src_MD - the MD-version source directory, single chains.
+
+src_MD-M - the MD-version source directory, oligomeric proteins
+
+bin - the binaries/scripts directory; its BATCH_SCRIPTS directory contains the
+ batch scripts (at present the only example is for PBS: unres_3P_PBS.csh,
+ which is an UNRES calling script and start.mat, which is the batch script
+ submitted to the PBS system).
+
+doc - documentation (this file and EXAMPLES.TXT)
+
+examples - sample input files (see EXAMPLES.TXT for description).
+
+To produce the executable do the following:
+
+a) To build parallel version, make sure that MPI is installed in your system.
+ Note that the package will have limited functions when compiled in a single-CPU mode.
+ On linux cluster the command source $HOME/.env should be added to .tcshrc
+ or equivalent file to use parallel version of the program, the
+ alternative is to use queuing system like PBS.
+ In some cases the FORTRAN library subroutine GETENV does not work properly
+ with MPI, if the script is run interactively. In such a case try to
+ add the source mygentenv.F and turn on the -DMYGETENV preprocessor flag.
+
+b) Change directory to the respective source directory.
+
+c) Edit the appropriate Makefile (parallel program that includes CSA
+ procedure, the serial version is no longer supported, for serial task
+ parallel program can be run using only one processor) to customize to your
+ system. Makefiles for the following systems are provided:
+
+ Makefile_osf_f90 - OSF1/Tru64 UNIX HP Alphaserver with f90 compiler,
+ Makefile_lnx_pgf90 - Linux, the pgf90 compiler,
+ Makefile_lnx_ifc - Linux, ifc compiler.
+ Makefile_win_pgf90 - Windows, the pgf90 compiler.
+
+ Other systems should not cause problems; all you have to do is to change
+ the compiler, compiler options, and preprocessor options. Also, change the
+ BIN variable, if you want to put your binaries in other place than
+ PROTARCH/BIN. In the case of Makefile make sure that the MPI directories are
+ correctly specified.
+
+ The following architectures are defined in the .F source files:
+
+ AIX - AIX systems (put -DAIX as one of the preprocessor options, if
+ this is your system)
+
+ LINUX - Linux (put -DLINUX)
+
+ G77 - Gnu-Fortran compilers (might require sum moderate source code editing)
+ (put -DG77). The recommended compiler is gfortran and not g77.
+
+ PGI - PGI compilers
+
+ WINPGI - additional setting for PGI compilers for MS Windows
+
+ SGI - all SGI platforms; should also be good for SUN platforms (put -DSGI)
+
+ WIN - MS Windows with Digital Fortran compiler (put -DWIN)
+
+ For other platforms, the only problems might appear in connection with
+ machine-specific I/O instructions. Many files are opened in the append
+ mode, whose specification in the OPEN statement is quite machine-dependent.
+ In this case you might need to modify the source code accordingly.
+ The other platform dependent routines are the timing routines contained
+ in timing.F. In addition to the platforms specified above, ES9000, SUN,
+ KSR, and CRAY are defined there.
+
+ For parallel build -DMP and -DMPI must be set (these are set in Makefile).
+
+ IMPORTANT! Apart from this, two define flags: -DCRYST_TOR and -DMOMENT
+ define earlier versions of the force field. The MUST NOT be entered, if
+ the CASP5 and later versions of the force field are used.
+
+d) Build the unres executables by typing at your UNIX prompt:
+
+ make # will build unres
+
+ make clean # will remove the object files
+
+ The bin directory contains pre-built binaries for Red Hat Linux. These
+ executables are specified in the csh scripts listed in section 4.
+
+e) Customize the C-shell scripts unres.unres (to run the parallel version on
+ set of workstation). See the next section of this manual for guidance.
+
+After the executables are build and C-shell scripts customized, you can run the
+test examples contained in UNRES/examples.
+
+5. CUSTOMIZING YOUR C-SHELL SCRIPT
+----------------------------------
+
+IMPORTANT NOTE - The unres.csh script is for Linux and should also be easily
+adaptable to other systems running MPICH. This script is for interactive
+parallel jobs. Examples of scripts compatible with PBS (pbs.sub) and LoadLever
+(sp2.sub) queuing systems are also provided.
+
+Edit the following lines in your unres.csh script:
+
+set DD = your_database_directory
+
+e.g., if you installed the package on the directory /usr/local, this line
+looks like this:
+
+set DD = /usr/local/UNRES/PARAM
+
+set BIN = your_binaries_directory
+
+set FGPROCS = number_of_processors_per_energy/force_evaluation (MD)
+
+e.g., if the root directory is as above:
+
+set BIN = /usr/local/UNRES/bin
+
+6. COMMAND LINE AND FILES
+-------------------------
+
+To run UNRES interactively enter the following command at your Unix prompt
+or put it in the batch script:
+
+unres.csh POTENTIAL INPUT N_PROCS
+
+where:
+
+POTENTIAL specifies the side-chain interaction potential type and must be
+one of the following:
+
+LJ - 6-12 radial Lennard-Jones
+LJK - 6-12 radial Lennard-Jones-Kihara (shifted Lennard Jones)
+BP - 6-12 anisotropic Berne-Pechukas based on Gaussian overlap (dilated
+ Lennard-Jones)
+GB - 6-12 anisotropic Gay-Berne (shifted Lennard-Jones)
+GBV - 6-12 anisotropic Gay-Berne-Vorobjev (shifted Lennard-Jones)
+
+See section 4. (Force Fields) for explanation and usage.
+
+At present, only the LJ and GB potentials are applied. The LJ potential
+is used in the "CASP3" version of the UNRES force field that is able
+to predict only alpha-helical structures. All further version of the
+UNRES force field use the GB potential. For the description of all above-mentioned
+potentials see A. Liwo, St. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky,
+H.A. Scheraga, J. Comput. Chem., 1997, 18, 849-873.
+
+INPUT is the prefix for input and output files (see below)
+
+N_PROCS is the number of processors; for a CSA or REMD/MREMD run it MUST be at least 2.
+
+Note! The script takes one more variable, FGPROCS, as the fourth argument,
+which is the number of fine-grain processors to parallelize energy
+evaluations. The corresponding code is in UNRES/CSA, but it was written
+using MPL instead of MPI and therefore is never used in the present version.
+At present we have no plans to rewrite fine-grain parallelization using MPI,
+because we found that the scalability for up to 200 residue polypeptide
+chains was very poor, due to a small number of interactions and,
+correspondingly, unfavorable ratio of the overhead to the computation time.
+
+INPUT.inp contains the main input data and the control parameters of the CSA
+ method.
+
+INPUT.out_POTENTIAL_xxx - main output files from different processors; xxx
+ denotes the number of the processor
+
+INPUT_POTENTIALxxx.stat - summary files with the energies, energy components,
+ and RMS deviations of the conformations produced by each of the processors;
+ not used in CSA runs; also it outputs different quantity in MD/MREMD runs.
+
+CSA version specific files:
+
+INPUT_POTENTIALxxx.int - internal coordinates; in the CSA run
+ INPUT_POTENTIAL_000.int contains the coordinates of the conformations,
+ and the other files are empty
+
+INPUT.CSA.history - history file from a CSA run. This is an I/O file, because
+ it can be used to restart an interrupted CSA run.
+
+INPUT.CSA.seed - stores the random seed generated in a CSA run; written for
+ restart purposes.
+
+INPUT.CSA.bank - current bank of conformations obtained in CSA calculations
+ (expressed as internal coordinates). This information is also stored in
+ INPUT_POTENTIAL000.int
+
+INPUT.CSA.rbank - as above, but contains random-generated conformations.
+
+MD version specific files:
+
+INPUT_MDyyy.pdb - Cartesian coordinates of the conformations in PDB format.
+
+INPUT_MDyyy.x - Cartesian coordinates of the conformations in ASCII format.
+
+INPUT_MDyyy.cx - Cartesian coordinates of the conformations in compressed format
+ (need xdr2pdb to convert to PDB format).
+
+The program currently produces some more files, but they are not used
+for any purposes and most of them are scratched after a run is completed.
+
+The run script also contains definitions of the parameter files through the
+following environmental variables:
+
+SIDEPAR - parameters of the SC-SC interaction potentials (U_{SC SC});
+SCPPAR - parameters of the SC-p interaction potential (U_{SCp}); this file can
+ be ignored by specifying the -DOLDSCP preprocessor flag, which means that the
+ built-in parameters are used; at present they are the same as the parameters
+ in the file specified by SCPPAR;
+ELEPAR - parameters of the p-p interaction potentials (U_{pp});
+FOURIER - parameters of the multibody potentials of the coupling between the
+ backbone-local and backbone-electrostatic interactions (U_{corr});
+THETPAR - parameters of the virtual-bond-angle bending potentials (U_b);
+ROTPAR - parameters of the side-chain rotamer potentials (U_{rot});
+TORPAR - parameters of the torsional potentials (U_{rot});
+TORDPAR - parameters of the double-torsional potentials.
+SCCORPAR - parameters of the supplementary torsional sequence-specific potentials
+ (not implemented yet).
+
+7. FORCE FIELDS
+---------------
+
+UNRES is being developed since 1997 and several versions of the force field
+were produced. The settings and references to these force fields are
+summarized below.
+
+Force fields for CSA version (can be used in MD but haven't been parameterized for this
+purpose).
+
+---------------------------------------------------------------------------------------
+ Additional SC-SC Example script Structural
+Force field compiler flags potential and executables classes covered References
+ (Linux; PGF90
+ and IFC)
+---------------------------------------------------------------------------------------
+
+CASP3 -DCRYST_TOR LJ unres_CASP3.csh only alpha [1-3]
+ -DCRYST_BOND unres_pgf90_cryst_tor.exe
+ -DCRYST_THETA unres_ifc6_cryst_tor.exe
+ -DCRYST_SC
+ -DMOMENT
+
+ALPHA -DMOMENT GB unres_CASP4.csh only alpha [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+BETA -DMOMENT GB unres_CASP4.csh only beta [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+ALPHABETA -DMOMENT GB unres_CASP4.csh all [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+CASP5 -DCRYST_BOND GB unres_CASP5.csh all [7,8,11]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+
+3P -DCRYST_BOND GB unres_3P.csh all [12,13]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+
+4P -DCRYST_BOND GB unees_4P.csh all [12,13]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+---------------------------------------------------------------------------------------
+
+Force fields for MD version
+
+---------------------------------------------------------------------------------------
+ Additional SC-SC Example script Structural
+Force field compiler flags potential and executables classes covered References
+ (Linux; PGF90
+ and IFC)
+---------------------------------------------------------------------------------------
+
+GAB -DCRYST_BOND GB unres_GAB.csh mostly alpha [19]
+ -DCRYST_THETA
+ -DCRYST_SC
+
+E0G -DCRYST_BOND GB unres_E0G.csh mostly alpha [19]
+ -DCRYST_THET
+ -DCRYST_SC
+
+1L2Y_1LE1 none GB unres_ab.csh all [20,25-27]
+
+---------------------------------------------------------------------------------------
+
+The example scripts (the *.csh filed) contain all appropriate parameter files, while
+the energy-term weights are provided in the example input files listed in EXAMPLES.TXT
+(*.inp; see section 5. for description of the input files). However, it is user's
+responsibility to specify appropriate compiler flags. Note that a version WILL NOT work,
+if the force-field specific compiler flags are not set. The parameter files specified
+in the run script also must strictly correspond to the energy-term weights specified in
+the input file. The parameter files for specific force fields are also specified below
+and the energy-term weights are specified in section 5.
+
+The parameter files are as follows (the environment variables from section 3 are
+used to identify the parameters):
+
+CASP3:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_cryst.parm
+TORDPAR torsion_double_631Gdp.parm (not used)
+SIDEPAR scinter_LJ.parm
+ELEPAR electr.parm
+SCPPAR scp.parm
+FOURIER fourier_GAP.parm (not used)
+SCCORPAR rotcorr_AM1.parm (not used)
+
+ALPHA, BETA, ALPHABETA (CASP4):
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_ecepp.parm
+TORDPAR torsion_double_631Gdp.parm (not used)
+SIDEPAR scinter_GB.parm
+ELEPAR electr.parm
+SCPPAR scp.parm
+FOURIER fourier_GAP.parm
+SCCORPAR rotcorr_AM1.parm (not used)
+
+CASP5:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR scinter_GB.parm
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_iter7n_c
+SCCORPAR rotcorr_AM1.parm (not used)
+
+3P:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.3P7_iter81_1r
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm (not used)
+
+4P:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.4P5_iter33_3r
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm (not used)
+
+GAB:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+E0G:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+1L2Y_1LE1:
+
+BONDPAR bond_AM1.parm
+THETPAR theta_abinitio.parm
+ROTPAR rotamers_AM1_aura.10022007.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR scinter_${POT}.parm
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+Additionally, for 1L2Y_1LE1, the following environment variables and files are required
+to generate random conformations:
+
+THETPARPDB thetaml.5parm
+ROTPARPDB scgauss.parm
+
+For CSA, the best force field is 4P. For MD, the 1L2Y_1LE1 force field is best for
+ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
+overemphasizes beta structures and has to be run with secondary-structure-prediction
+information. For prediction of the structure of mostly alpha-protein, and for running
+dynamics of large proteins, the best is the GAB force field. All these force fields
+were trained by using our procedure of hierarchical optimization [5].
+The 4P and 1L2Y_1LE1 force fields have considerable power independent of structural class.
+The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
+and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
+predicts reasonably the structure of alpha-helical proteins and is still not obsolete,
+while for beta and alpha+beta structure prediction
+3P or 4P should be used, because they are cheaper and more reliable than BETA and
+ALPHABETA. The early CASP3 force field is included for historical reasons only.
+
+7. INPUT FILES
+--------------
+
+7.1. Main input data file
+-------------------------
+
+Most of the data are organized as data lists, where the data can be put
+in any order, using a series of statements of the form:
+
+KEYWORD=value
+
+for simple non-logical variables
+
+or just
+
+KEYWORD
+
+to indicate that the corresponding option is turned on. For array variables
+the assignment statement is:
+
+KEYWORD=value1,value2,...
+
+However, the data lists are unnamed and that must be placed EXACTLY in the
+order indicated below. The presence of an "&" in the 80th column of a line
+indicates that the next line will belong to the same data group. The parser
+subroutines that interpret the keywords are case insensitive.
+
+Each group of data organized as a data list is indicated as "data list format"
+input.
+
+8.1.1. Title
+------------
+Any string containing up to 80 characters. The first input line is always
+interpreted as title.
+
+8.1.2. Control data (data list format; READ_CONTROL subroutine)
+---------------------------------------------------------------
+
+8.1.2.1 Keywords to chose calculation type
+------------------------------------------
+
+OUT1FILE - only the master processor prints the output file in a parallel job
+
+MINIMIZE - if present, energy minimization will be carried out.
+
+REGULAR - regularize the read in conformation (usually a crystal or
+ NMR structure) by doing a series of three constrained minimizations,
+ to keep the structure as close as possible to the starting
+ (experimental) structure. The constraints are the CA-CA distances
+ of the initial structure. The constraints are gradually diminished
+ and removed in the last minimization.
+
+SOFTREG - regularize the read in conformation (usually a crystal or NMR
+ structure) by doing a series of constrained minimizations, with
+ additional use of soft potential and secondary structure
+ freezing, to keep the structure as close as possible to the
+ starting (experimental) structure.
+
+
+CSA - if present, the run is a CSA run. At present, this is the only
+ reliable mode of doing global conformational search with this
+ package; it is NOT recommended to use MCM or THREAD for this
+ purpose.
+
+MCMA - if present, this is a Monte Carlo Minimization (MCM) run.
+
+MULTCONF- if present, conformations will be read from the INPUT.intin
+ file.
+
+MD - run canonical MD (single or multiple trajectories)
+
+RE - run REMD or MREMD (parallel jobs only)
+
+MUCA - run multicanonical MD calculations (parallel jobs only)
+
+MAP=number (integer)
+Conformational map will be calculated in chosen angles.
+
+THREAD=number (integer)
+Threading or threading-with-minimization run, using a database of structures
+contained in the $DD/patterns.cart pattern data base (502 chains or chain
+fragments), using a total number patterns. It is recommended to use this with
+energy minimization; this implies regularization of each minimized pattern.
+For references see A. Liwo, M.R. Pincus, R.J. Wawak,
+S. Rackovsky, St. Oldziej, H.A. Scheraga, J. Comput. Chem., 1997, 18, 874-887
+and A. Liwo, St. Oldziej, R. Kazmierkiewicz, M. Groth, C. Czaplewski,
+Acta Biochim. Pol., 1997, 44, 527-547.
+
+CHECKGRAD - compare numerical and analytical gradient; to be followed by:
+ CART - energy gradient in virtual-bond vectors (Cartesian coordinates)
+ INT - energy gradient in internal coordinates (default)
+ CARINT - derivatives of the internal coordinates in the virtual-bond vectors.
+
+8.1.2.2 Specification of protein and structure output in non-MD applications
+----------------------------------------------------------------------------
+
+ONE_LETTER - one-letter and not three-letter code of the amino-acid residues
+ is used
+
+SYM (1) - number of chains with same sequence (for oligomeric proteins only),
+
+PDBSTART - the initial conformation is read in from a PDB file
+
+UNRES_PDB - the starting conformation is in UNRES representation (Calpha
+ and SC coordinates only). This keyword MUST appear in such a case
+ or the program will generate erroneous and unrealistic side-chain
+ coordinates.
+
+RAND_CONF- start from a random conformation
+
+EXTCONF - start from an extended chain conformation
+
+PDBOUT - if present, conformations will be output in PDB format. Note that
+ this keyword affects only the output from single energy evaluation,
+ energy minimization and multiple-conformation data. To request
+ conformations from MD/MREMD runs in PDB format, the MDPDB keyword
+ must be placed on the MD input record.
+
+MOL2OUT - if present, conformations will be output in SYBYL mol2 format
+
+REFSTR - if present, reference structure will be read (e.g., to monitor
+ the RMS deviation from the crystal structure)
+
+PDBREF - if present, a reference structure will be read in to compare
+ the calculated conformations with it
+
+UNRES_PBD - the starting/reference structure is read from an UNRES-generated
+ PDB file
+
+Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
+Output mode for MD version is specified in MD input (see section 5.5).
+
+8.1.2.3. Miscellaneous
+----------------------
+
+CONSTR_DIST=number
+0 - no distance restraints
+>0 imposes harmonic restraints on selected distances; see section 5.12.
+In MD version, also restraints on the q variable [18] can be used.
+
+WEIDIS=number (real)
+the weight of the distance term; applies for REGULARIZE and THREAD, otherwise
+ignored.
+
+USE_SEC_PRED - use secondary-structure prediction information.
+
+SEED=number (integer) (no default)
+Random seed (required, even if the run is not a CSA, MCM, MD or MREMD run)
+
+PHI - only the virtual-bond dihedral angles gamma are considered as
+ variables in energy minimization
+
+BACK - only the backbone virtual angles (virtual-bond angles theta and
+ virtual-bond dihedral angles gamma) are considered as variables
+ in energy minimization
+
+By default, all internal coordinates: theta, gamma, and the side-chain
+centroid polar angles alpha and beta are considered as variables in energy
+minimization.
+
+RESCALE_MODE=number (real)
+Choice of the type of temperature dependence of the force field.
+0 - no temperature dependence
+1 - homographic dependence (not implemented yet with any force field)
+2 - hyperbolic tangent dependence [18].
+
+T_BATH=number (real)
+temperature (for MD runs and temperature-dependent force fields).
+
+The following keywords apply to MCM only:
+
+MAXGEN=number (integer) (10000)
+maximum number of conformations generated in a single MCM iteration
+
+MAXOVERLAP=number (integer) (1000)
+maximum number of conformations with "bad" overlaps allowed to appear in a
+row in a single MCM iteration.
+
+DISTCHAINMAX - (multi-chain capacity only) maximum distance between the
+ last residue of a given chain and the first residue of the
+ next chain such that restraints will not be imposed; quartic
+ restraints will be imposed for greater distances.
+
+ENERGY_DEC - detailed energies will be printed for each interacting pair
+ or each virtual bond, virtual-bond angle and dihedral angle,
+ side chain, etc. DO NOT use unless a single energy evaluation
+ was requested.
+
+8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+-----------------------------------------------------------
+
+This data group is present, if MINIMIZE was specified on the control card.
+Otherwise, it must not appear.
+
+CART - minimize in virtual-bond vectors instead of angles
+
+MAXMIN=number (integer) (2000)
+maximum number of iterations of the SUMSL minimizer
+
+MAXFUN=number (integer) (5000)
+maximum number of function evaluations in a single minimization
+
+TOLF=number (real) (1.0e-2)
+Tolerance on function
+
+RTOLF=number (real) (1.0d-4)
+Relative tolerance on function
+
+The SUMSL minimizer is used in UNRES/CSA. For detailed description of
+the control parameters see the source file cored.f and sumsld.f
+
+
+8.1.4 CSA control parameters
+----------------------------
+
+This data group should be present only, if CSA was specified on the control
+card. It is recommended that the readers to read publications on CSA method
+for more complete description of the parameters. Brief description of
+parameters:
+
+NCONF=number (integer) (50)
+This corresponds to the size of the bank at the beginning of the
+CSA procedure. The size of the bank, nbank, is set to nconf.
+If necessary (at much later stages of the CSA: see icmax below),
+nbank increases by multiple of nconf.
+
+JSTART=number (integer) (1)
+JEND=number (integer) (1)
+This corresponds to the limit values of do loop, each of which
+corresponds to an separate CSA run. If jstart=1, and jstart=100,
+this routine will repeat 100 separate CSA runs (limited by CPU)
+each one with separate random number initialization.
+The only difference between two CSA runs (one with jstart=jend=1
+and another one with jstart=jend=2) would be different random
+number initializations if other parameters are identical.
+
+NSTMAX=number (integer) (500000)
+This is to set a limit the total number of local minimizations of CSA
+before termination.
+
+N1=number (integer) (6)
+N2=number (integer) (4)
+N3=number (integer) (0)
+N4=number (integer) (0)
+N5=number (integer) (0)
+N6=number (integer) (10)
+N7=number (integer) (0)
+N8=number (integer) (0)
+N9=number (integer) (0)
+IS1=number (integer) (1)
+IS2=number (integer) (8)
+These numbers are used to generate trial conformations for each seed.
+See the file, "newconf.f", for more details.
+ n1: the total number of trial conformations for each seed by substituting
+ nran number of variable angles (see subroutine newconf1ab and
+ subroutine newconf1ar)
+ n2: the total number of trial conformations for each seed by substituting
+ nran number of groups of variable angles (see subroutine newconf1bb and
+ subroutine newconf1br)
+ n3: the total number of trial conformations for each seed by substituting
+ a window of residues which forms a beta-hairpin, if there is no enough
+ beta-hairpins uses the same algorithm as n6
+ n4: the total number of trial conformations for each seed by shifting the
+ turn in beta-hairpin by +/- 1 or 2 residues, if there is no enough
+ beta-hairpins uses the same algorithm as n6
+ n5: not used
+ n6: the total number of trial conformations for each seed by substituting
+ a window of residues [is1,is2] inclusive. The size of the window is
+ determined in a random fashion (see subroutine newconf_residue for
+ generation of the trial conformations)
+ n7: the total number of trial conformations for each seed by copying a
+ remote strand pair forming nonlocal beta-sheet contact
+ n8: the total number of trial conformations for each seed by copying an
+ alpha-helical segment
+ n9: the total number of trial conformations for each seed by shifting the
+ alpha-helical segment by +/- 1 or 2 residues
+
+Typical values used for a 75-residue helical protein is
+(6 4 0 0 0 10 1 26) for (n1,n2,n3,n4,n5,n6,is1,is2), respectively.
+In this example, a total of 20 trial conformations are generated for a seed
+Usually is1=1 is used for all applications, and the value of is2 is set about
+to 1/3 of the total number of residues. n3, n4 and n7 are design to help in
+case of proteins with beta-sheets
+
+NRAN0=number (integer) (4)
+NRAN1=number (integer) (2)
+IRR=number (integer) (1)
+These numbers are used to determine if the CSA stage is very early.
+One can use (4 2 1) for these values. For more details one should look into
+the file, "newconf.f", for more details.
+
+NTOTAL=number (integer) (10000)
+CUT1=number (real) (2.0)
+CUT2=number (real) (5.0)
+Annealing schedule is set in following fashion.
+The value of D_cut is reduced geometrically from 1/cut1 of D_ave (at the
+beginning) to 1/cut2 of D_ave (after ntotal number of minimizations) where
+D_ave is the average distance between two conformations in the First_bank.
+
+ESTOP=number (real) (-3000.0)
+The CSA procedure stops if a conformations with energy lower than estop is
+obtained. If the do-loop set by jstart and jend requires more than one loop,
+the program will go on until the do-loop is finished.
+
+ICMAX=number (integer) (3)
+The maximum value of cycle (see the original publications for details).
+If the number of cycle exceeds this value the program will add nconf
+more conformations to Bank and First_bank to continue CSA procedure if
+the new size of the nbank is within the maximum set by nbankm (see above).
+If the size of nbank exceeds the maximum set by nbankm the CSA procedure
+for this run will stop and next CSA will begin depending on the do-loop
+set by jstart and jend.
+
+IRESTART=number (integer) (0)
+This tells you if the run is fresh start (irestart=0) or a restart (irestart=1)
+starting from an old results
+
+NDIFF=number (integer) (2)
+The number of variables use in comparison when structure is added to the
+bank,4 - all angels, 2 - only backbone angles gamma and theta
+
+NBANKTM=number (integer) (0)
+The maximum number of structures saved in *.CSA.bankt as history of the run
+Do not use bankt on massively parallel computation as it kills scalability.
+
+DELE=number (real) (20.0)
+Energy cutoff for bankt.
+
+DIFCUT=number (real) (720.0)
+Angle cutoff for bankt.
+
+IREF=number (integer) (0)
+0 - normal run, 1 - local CSA which generates only structures close to the
+reference one read from *.CSA.native.int file
+
+RMSCUT=number (real) (4.0)
+CA RMSD cut off used in local CSA
+
+PNCCUT=number (real) (0.5)
+Percentage of native contact used in local CSA
+
+NCONF_IN=number (integer) (0)
+The number of conformation read for the first bank from the input file
+*.intin
+
+Optionally, the CSA parameters can be read from file INPUT.CSA.in, if
+this file exists. If so, they are read in free format in the following
+order:
+
+nconf
+jstart,jend
+nstmax
+n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
+nran0,nran1,irr
+nseed
+ntotal,cut1,cut2
+estop
+icmax,irestart
+ntbankm,dele,difcut
+iref,rmscut,pnccut
+ndiff
+
+
+8.1.5. MCM data (data list, subroutine MCMREAD)
+-----------------------------------------------
+
+This data group is present, if MCM was specified on the control card.
+Otherwise it must not appear.
+
+MAXACC=number (integer) (100)
+Maximum number of accepted conformations
+
+MAXTRIAL=number (integer) (100)
+Maximum number of unsuccessful trials in a row
+
+MAXTRIAL_ITER=number (integer) (1000)
+Maximum number of unsuccessful trials in a single iteration
+
+MAXREPM=number (integer) (200)
+Maximum number of repetitions of the same minimum
+
+RANFRACT=number (real) (0.5d0)
+Fraction of chain-rebuild motions
+
+OVERLAP=number (real) (1.0d3)
+Bad contact energy criterion
+
+NSTEPH=number (integer) (0)
+Number of heating step in adaptive sampling
+
+NSTEPC=number (integer) (0)
+Number of cooling step in adaptive sampling
+
+TMIN=number (real) (298.0d0)
+Minimum temperature in adaptive-temperature sampling)
+
+TMAX=number (real) (298.0d0)
+Maximum temperature in adaptive-temperature sampling)
+
+The temperature is changed according to the formula:
+
+T = TMIN*EXP(ISTEPH*(TMAX-TMIN)/NSTEPH) when heating
+
+and
+
+T = TMAX*EXP(-ISTEPC*(TMAX-TMIN)/NSTEPC) when cooling
+
+The default is to use a constant temperature.
+
+NWINDOW=number (integer) (0)
+Number of windows in which the variables will be perturbed; the windows are
+defined by the numbers of the respective amino-acid residues. If NWINDOW
+is nonzero, after specifying all MCM input the next lines must define the
+windows. Each line looks like this:
+
+winstart winend (free format)
+
+e.g. if NWINDOW=2, the input:
+
+4 10
+15 20
+
+will mean that only the variables of residues 4-10 and 15-20 will be perturbed.
+However, in general, all variables will be considered in minimization.
+
+PRINT_MC=number (0)
+Printout level in MCM. 0 - no intermediate printing, 1 and 2 - moderate
+printing, 3 - extensive printing.
+
+NO_PRINT_STAT - no output to INPUT_POTENTIALxxx.stat.
+
+NO_PRINT_INT - no internal-coordinate output to INPUT_POTENTIALxxx.int.
+
+8.1.6. MD data (subroutine READ_MDPAR)
+--------------------------------------
+
+NSTEP (1000000) number of time steps per trajectory.
+
+NTWE (100) NTWX (1000) frequency of energy and coordinate output, respectively.
+The coordinates are dumped in the pdb or compressed Gromacs (cx) format,
+depending on the next keyword.
+NTWE=0 means no energy dump.
+
+MDPDB - dump coordinates in the PDB format (cx otherwise)
+
+TRAJ1FILE only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+REST1FILE only the master writes the restart file
+
+DT (real) (0.1) time step; the unit is "molecular time unit" (mtu); 1 mtu = 48.9 fs
+
+DAMAX (real) (1.0) maximum allowed change of acceleration during a single time step.
+The time step gets scaled down, if this is exceeded.
+
+DVMAX (real) (20.0) maximum allowed velocity (in A/mtu)
+
+EDRIFTMAX (real) (10.0) maximum allowed energy drift in a single MD step (10 kcal/mol)
+
+REST restart flag. The calculation is restarted if present.
+
+LARGE very detailed output. Don't use except for debugging.
+
+PRINT_COMPON prints energy components.
+
+RESET_MOMENT (1000) frequency of zeroing out the total angular momentum when
+running Berendsen mode calculations (for Langevin calculations meaningless).
+
+RESET_VEL=number (integer) (1000) - frequency of resetting velocities to values
+from Gaussian distribution.
+
+RATTLE - use RATTLE algorithm (constraint bonds); not yet implemented.
+
+RESPA - use the Multiple Time Step (MTS) or Adaptive Multiple Time Step (A-MTS)
+algorithm [17]. Without this flag the variable time step (VTS) [14] is run.
+
+NTIME_SPLIT=number (integer) (1) - initial number of time-split steps
+
+MAXTIME_SPLIT=number(integer) (64) - maximum number of time-split step
+
+If NTIME_SPLIT==MAXTIME_SPLIT, MTS is run.
+
+R_CUT=number (real) (2.0) - the cut-off distance in splitting the forces into short- and
+long-range in site-site VDW distance units.
+
+LAMBDA (real) (0.3) - the transition length (in site-site VDW distance units) between
+short- and long-range forces.
+
+XIRESP - flag to use MTS/A-MTS with Nose-Hoover/Nose-Poincare thermostats.
+
+LANG=number (integer) (0) Langevin dynamics flag:
+
+0 - No explicit Langevin dynamics.
+1 - Langevin with direct integration of the equations of motion (recommended
+ for Langevin calculations)
+2 - Langevin calculation with analytical pre-integration of the friction and
+ stochastic part of the equations of motion using an algorithm adapted from TINKER.
+ This is MUCH MORE time- and memory-consuming than 1 and requires compiling without
+ the -DLANG0 flag and enormously increases memory requirements.
+3 - The stochastic integrator developed by Cicotti and coworkers.
+4 - for other stochastic integrators (not used at present).
+
+Note: With the enclosed code, the -DLANG0 compiler flag is included which disables
+LANG=2 and LANG=3
+
+TBF Berendsen thermostat.
+
+TAU_BATH (1.0) (units are mtus; 1mtu=48.9 fs) constant of the coupling to the thermal bath
+ used with the Berendsen thermostat.
+
+NOSEPOINCARE99 - the Nose-Poincare thermostat as of 1999 will be used.
+
+NOSEPOINCARE01 - the Nose-Poincare thermostat as of 2001 will be used.
+
+NOSEHOOVER96 - the Nose-Hoover thermostat will be used.
+
+Q_NP=number (real) (0.1) - the value of the mass of the fictitious particle in the calculations
+ with the Nose-Poincare thermostat.
+
+T_BATH (300.0) (in K) temperature of canonical simulation or temperature to generate
+velocities.
+
+ETAWAT (0.8904) viscosity of water (in centipoises)
+
+RWAT (1.4) radius of water molecule (in A)
+
+SCAL_FRIC=number (real) (0.02) - scaling factor of the friction coefficients.
+
+SURFAREA - scale friction acting on atoms by atoms' solvent accessible area.
+
+RESET_FRICMAT=number (integer) (1000) - recalculate friction matrix every RESET_FRICMAT MD steps.
+
+USAMPL restraints on q (see reference 5 for meaning) will be imposed (see section .
+In this case, the next records specify the restraints; these records are
+placed before the list of temperatures or numbers of trajectories.
+
+EQ_TIME=number (real) (1.0e4) time (in mtus; 1 mtu=48.9 fs) after which restraints
+on q will start to be in force.
+
+If USAMPL has been specified, the following information must be supplied after the
+main MD input data record (subroutine READ_FRAGMENTS):
+
+Line 1: nset, npair, nfrag_back (number of sets of restraints, number of restrained
+fragments, number of restrained pairs, number of restrained backbone fragments
+(in terms of theta and gamma angles)
+
+For each set of restraints (1, 2,..., nset):
+
+mset(iset) - how many times the set is multiplied
+
+wfrag(i,iset), ifrag(1,i,iset), ifrag2(2,i,iset),qfrag(i,iset)
+weight of the restraint, first and last residue of the fragment, target q value.
+This information is repeated through nfrag.
+
+wpair(i,iset), ipair(1,i,iset), ipair(2,i,iset),qinpair(i,iset)
+weight of the restraint, first and second fragment of the pair (according to fragment
+list), target q value. This information is repeated through npair
+
+wfrag_back(1,i,iset), wfrag_back(2,i,iset), wfrag_back(3,i,iset),
+ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+weight of the restraints on theta angles, weight on the restraints on gamma angles,
+weight of the restraints on side-chain rotamers, first residue of the fragment,
+last residue of the fragment. This information is repeated through nfrag_back.
+
+8.1.7 REMD/MREMD data (subroutine READ_REMDPAR)
+-----------------------------------------------
+
+NREP (3) number of replicas in a REMD/MREMD run
+
+NSTEX (1000) number of steps after which exchange is performed in REMD/MREMD
+ runs
+
+The temperatures in replicas can be specified through
+
+RETMIN (10.0) minimum temperature in a REMD/MREMD run
+
+RETMAX (1000.0) maximum temperature in a REMD/MREMD run
+
+Then the range from retmin to retmax is divided into equal segments and
+temperature of the replicas assigned accordingly,
+
+or
+
+TLIST means that the NREP temperature of the replicas will be input in the
+next record
+
+MLIST numbers of trajectories per each of the NREP temperatures will be
+specified in the record after the list of temperatures; this specifies
+a MREMD run.
+
+Important! The number of processors must be exactly equal to the number of
+trajectories, i.e., NREP for a REMD run or sum_i mlist(i) for a MREMD run.
+
+SYNC - all trajectories will be synchronized every NSTEX time steps
+(by default, they are not synchronized)
+
+TRAJ1FILE only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+REST1FILE only the master writes the restart file
+
+HREMD - Hamiltonian replica exchange flag; not only temperatures but also
+sets energy-term weights are exchanged between conformations.
+
+TONLY - run a "fake" HREMD with many sets of energy-term weights in a
+single run but only temperature exchange.
+
+8.1.8 Energy-term weights (data list; subroutine MOLREAD)
+---------------------------------------------------------
+
+WLONG=number (real) (1.0d0)
+common weight of the U(SC-SC) (side-chain side-chain interaction)
+and U(SC,p) (side-chain peptide-group) term
+
+WSCC = number (real) (WLONG)
+weight of the U(SC-SC) term
+
+WSCP = number (real) (WLONG)
+weight of the U(SC-p) term
+
+WELEC=number (real) (1.0d0)
+weight of the U(p-p) (peptide-group peptide-group interaction) term
+
+WEL_LOC=number (real) (1.0d0)
+weight of the U_el_loc^3 (local-electrostatic cooperativity, third-order) term
+
+WCORRH=number (real) (1.0d0)
+weight of the U(corr) (cooperativity of hydrogen-bonding interactions, fourth-order) term
+
+WCORR5=number (real) (0.0d0)
+weight of the U_el_loc^5 (local-electrostatic cooperativity, 5th order
+contributions)
+
+WCORR6=number (real) (0.0d0)
+weight of the U_el_loc^6 (local-electrostatic cooperativity, 6th order
+contributions)
+
+WTURN3=number (real) (1.0d0)
+weight of the U_turn^3 (local-electrostatic cooperativity within 3 residue
+segment, 3rd order contribution)
+
+WTURN4=number (real) (1.0d0)
+weight of the U_turn^4 (local-electrostatic cooperativity within 4 residue
+segment, 4rd order contributions)
+
+WTURN6=number (real) (1.0d0)
+weight of the U_turn^6 (local-electrostatic cooperativity within 6 residue
+segment, 6rd order contributions)
+
+WTOR=number (real) (1.0d0)
+weight of the torsional term U(tor)
+
+WANG=number (real) (1.0d0)
+weight of the virtual-bond angle bending term U(b)
+
+WSCLOC=number (real) (1.0d0)
+weight of the side-chain rotamer term U(SC)
+
+WSTRAIN=number (real) (1.0d0)
+scaling factor of the distance-constrain or disulfide-bond strain energy term
+
+SCALSCP=number (real) (1.0d0)
+scaling factor of U(SC,p); this is an alternative to specifying WSCP; in
+this case WSCP will be calculated as WLONG*SCALSCP
+
+SCAL14=number (real) (1.0d0)
+scaling factor of the 1,4 SC-p interactions
+
+CUTOFF (7.0) - cut-off on backbone-electrostatic interactions to compute 4-
+and higher-order correlations
+
+DELT_CORR (0.5) - thickness of the distance range in which the energy is
+decreased to zero
+
+The defaults are NOT the recommended values. No "working" default values
+have been set, because the force field is still under development. The values
+corresponding to the force fields listed in section 4 are as follows:
+
+CASP3:
+WELEC=1.5 WSTRAIN=1.0 WTOR=0.08617 WANG=0.10384 WSCLOC=0.10384 WCORR=1.5 &
+WTURN3=0 WTURN4=0 WTURN6=0 WEL_LOC=0 WCORR5=0 WCORR6=0 SCAL14=0.40 SCALSCP=1.0 &
+CUTOFF=7.00000 WSCCOR=0.0
+
+ALPHA:
+WSC=1.00000 WSCP=0.72364 WELEC=1.10890 WANG=0.68702 WSCLOC=1.79888 &
+WTOR=0.30562 WCORRH=1.09616 WCORR5=0.17452 WCORR6=0.36878 WEL_LOC=0.19508 &
+WTURN3=0.00000 WTURN4=0.55588 WTURN6=0.11539 CUTOFF=7.00000 WCORR4=0.0000 &
+WTORD=0.0 WSCCOR=0.0
+
+BETA:
+WSC=1.00000 WSCP=1.10684 WELEC=0.70000 WANG=0.80775 WSCLOC=1.91939 &
+WTOR=3.36070 WCORRH=2.50000 WCORR5=0.99949 WCORR6=0.46247 WEL_LOC=2.50000 &
+WTURN3=1.80121 WTURN4=4.35377 WTURN6=0.10000 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+
+ALPHABETA:
+WSC=1.00000 WSCP=1.43178 WELEC=0.41501 WANG=0.37790 WSCLOC=0.12880 &
+WTOR=1.98784 WCORRH=2.50526 WCORR5=0.23873 WCORR6=0.76327 WEL_LOC=2.97687 &
+WTURN3=0.09261 WTURN4=0.79171 WTURN6=0.01074 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+
+CASP5:
+WSC=1.00000 WSCP=1.54864 WELEC=0.20016 WANG=1.00572 WSCLOC=0.06764 &
+WTOR=1.70537 WTORD=1.24442 WCORRH=0.91583 WCORR5=0.00607 WCORR6=0.02316 &
+WEL_LOC=1.51083 WTURN3=2.00764 WTURN4=0.05345 WTURN6=0.05282 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+3P:
+WSC=1.00000 WSCP=2.85111 WELEC=0.36281 WANG=3.95152 WSCLOC=0.15244 &
+WTOR=3.00008 WTORD=2.89863 WCORRH=1.91423 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.72128 WTURN3=2.99827 WTURN4=0.59174 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+4P:
+WSC=1.00000 WSCP=2.73684 WELEC=0.06833 WANG=4.15526 WSCLOC=0.16761 &
+WTOR=2.99546 WTORD=2.89720 WCORRH=1.98989 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.60072 WTURN3=2.36351 WTURN4=1.34051 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+GAB:
+WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
+WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
+WVDWPP=0.11371 WHPB=1.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+E0G:
+WLONG=1.70905 WSCP=2.18310 WELEC=1.06684 WBOND=1.00000 WANG=1.17536 &
+WSCLOC=0.22070 WTOR=2.65798 WTORD=2.00646 WCORRH=0.23541 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.42789 WTURN3=1.68126 WTURN4=0.75080 WTURN6=0.00000 &
+WVDWPP=0.27044 WHPB=1.00000 WSCP14=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+1L2Y_1LE1:
+WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
+WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+-----------------------------------------------------------------------------
+
+If PDBSTART or PDBREF was specified in the control card, this line contains
+the PDB file name. Trailing slashes to specify the full path are permitted.
+The file name can contain up to 64 characters.
+
+8.1.10. Amino-acid sequence (free and text format)
+--------------------------------------------------
+
+This data appears, if PDBSTART was not specified, otherwise must not be present
+because the sequence would be taken from the PDB file. The first line contains
+the number of amino-acid residues, including the end groups (free format),
+the next lines contain the sequence in 20(1X,A3) format for the three-letter
+or 80A1 format for the one-letter code. There are two types of end-groups:
+Gly (three-letter code) or G (one-letter code), if an end group contains a full
+peptide bond (e.g., the acetyl N-terminal group or the carboxyamide C-terminal
+group) and D (in the three-letter code) or X (in the one-letter code), if the
+end group does not contain a peptide group (e.g., the NH2 N-terminal end group
+or the COOH C-terminal end group). (Note the Gly or G also denotes the regular
+glycine residue, if found in the middle of a chain).
+In the second case the end group is considered as a "dummy" group and serves
+only to define the first (last) virtual-bond dihedral angle gamma for the
+first (last) full amino-acid residue.
+
+Consider, for example, the Ac-Ala(19)-NHMe polypeptide. The three-letter code
+input will look like this:
+
+21
+ Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ Gly
+
+And the one-letter code input will be:
+
+21
+GAAAAAAAAAAAAAAAAAAAG
+
+If the sequence is changed to NH3(+)-Ala(19)-COO(-), the inputs will look
+like this:
+
+21
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ D
+
+and
+
+21
+XAAAAAAAAAAAAAAAAAAAX
+
+The sequence input is case-insensitive, because the present version of UNRES
+considers each amino-acid residue as an L-residue (there are no torsional
+parameters for the combinations of the D- and L-residues yet). Furthermore,
+each peptide group is considered as a trans group.
+
+If the version of UNRES has multi-chain capacity, placing a dummy residue
+inside the sequence indicates start of a new chain. For example, a system
+composed of two Ala(10) chains can be specified as follows (3-letter code):
+
+23
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D Ala Ala Ala Ala Ala Ala Ala Ala
+ Ala Ala D
+
+or (1-letter code)
+
+23
+XAAAAAAAAAAXAAAAAAAAAAX
+
+
+8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+--------------------------------------------------------------------------
+
+1st line:
+NS,(ISS(i),i=1,NS)
+
+NS - the number of half-cystines (required even if no half-cystines are present)
+
+ISS(i) - the position of ith half-cystine in the sequence (starting from the
+N-terminal end group)
+
+next line(s) (present only, if ns>0 and must not appear otherwise):
+NSS,(IHPB(i),JHPB(i),i=1,NSS)
+
+NSS - the number of disulfide bridges; must not be greater than NS/2
+
+IHPB(i),JHPB(i) - the cystine residue forming the ith bridge.
+
+The program will check, whether the residues specified in the ISS list
+are cystines and terminate with error, if any of them is not. The program
+also checks, if the numbers from the IHPB and the JHPB lists have appeared
+in the ISS list.
+
+8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+-----------------------------------------------------------------------
+
+This set of data specifies the harmonic constraints (if any) imposed on selected
+virtual-bond dihedral angles gamma.
+
+1st line:
+NDIH_CONSTR - the number of restrained gamma angles (required even if no
+restrains are applied).
+
+2nd line (present only, if NDIH_CONSTR > 0; must not appear otherwise):
+FTORS - the force constant expressed in kcal/(mol*rad**2)
+
+next NDIH_CONSTR lines (present only, if NDIH_CONSTR > 0):
+
+IDIH_CONSTR(i),PHI0(i),DRANGE(i)
+
+IDIH_CONSTR(i) - the number of ith restrained gamma angle. The angles are
+numbered after the LAST alpha-carbons. Thus, the first "real" angle has number
+4 and it corresponds to the rotation about the CA(2)-CA(3) virtual-bond axis
+and the last angle has the number NRES and corresponds to the rotation about
+the CA(NRES-2)-CA(NRES-1) virtual-bond axis.
+
+PHI0(i) - the "center" of the restraint (expressed in degrees)
+
+DRANGE(i) - the "flat well" range of the restraint (in degrees)
+
+The restraint energy for the ith restrained angle is expressed as:
+
+ /
+ | FTORS*(GAMMA(IDIH_CONSTR(i))-PHI0(i)+DRANGE(i))**2,
+ | if GAMMA(IDIH_CONSTR(i))<PHI0(i)-DRANGE(i)
+ |
+EDIH = < 0, if PHI0(i)-DRANGE(i) <= GAMMA(IDIH_CONSTR(i) <= PHI0(i)+DRANGE(i)
+ |
+ | FTORS*(GAMMA(IDIH_CONSTR(i))-PHI0(i)-DRANGE(i))**2,
+ | if GAMMA(IDIH_CONSTR(i))>PHI0(i)+DRANGE(i)
+ \
+
+Applying dihedral-angle constraints also implies that for ith constrained
+gamma angle the sampling be carried out from the
+[PHI0(i)-DRANGE(i)..PHI0(i)+DRANGE(i)] interval and not from the [-Pi..Pi]
+interval, if random conformations are generated. If only this and not
+restrained minimization is required, just set FTORS to 0.
+
+8.1.13 Distance restraints (subroutine READ_DIST_CONSTR)
+--------------------------------------------------------
+
+Restraints are imposed on Calpha...Calpha distances.
+
+NDIST=number (integer) (0) - number of restraints on specific distances.
+
+NFRAG=number (integer) (0) - number of distance-restrained protein segments.
+
+NPAIR=number (integer) (0) - number of distance-restrained pairs of segments.
+ Specifying NPAIR requires specification of segments.
+
+IFRAG=start(1),end(1),start(2),end(2)...start(NFRAG),end(NFRAG) (integers)
+First and last residues of the distance restrained segments.
+
+WFRAG=w(1),w(2),...,w(NFRAG) (reals) - force constants or bases for force
+constant calculation corresponding to fragment restraints.
+
+IPAIR=start(1),end(1),start(2),end(2),...,start(NPAIR),end(NPAIR) (integers)
+numbers of segments (consecutive numbers of start or end pairs in IFRAG
+specification), the distances between which will be restrained.
+
+WPAIR=w(1),w(2),...,w(NFRAG) (reals) - force constants or bases for force
+constant calculation corresponding to pair restraints.
+
+DIST_CUT=number (real) (5.0) - the cut-off distance in angstroms for force-
+constant calculations.
+
+The force constants within fragments/between pairs of fragments are calculated
+depending on the value of DIST_CONSTR described in section 5.1:
+
+1 - all force constants are equal to the respective entries of WFRAG/WPAIR
+
+2 - the force constants are equal to the respective entries of WFRAG/WPAIR
+ when the distance between the Calpha atoms in the reference structure
+ <=D_CUT, 0 otherwise.
+
+3 - the force constants are calculated from the formula:
+
+k(CA_j,CA_k)=W*exp{-[d(CA_j,CA_k)/DIST_CUT)]**2/2}
+
+where k(CA_j,CA_k) is the force constant between the respective Calpha atoms,
+d(CA_j,CA_k) is the distance between these Calpha atoms in the reference
+structure, and W is the basis for force-constant calculation (see above).
+
+If NDIST>0, the restraints on specific distance are subsequently input:
+
+ihpb(i), jhpb(i), forcon(i), i=1,NDIST
+
+where ihpb(i) and jhpb(i) are the numbers of the residues the distance
+between the Calpha atoms of which will be distance restrained and forcon(i)
+is the respective force constant.
+
+8.1.14 Internal coordinates of the reference structure (free format;
+--------------------------------------------------------------------
+ subroutine READ_ANGLES)
+ -----------------------
+
+This part of the data is present, if REFSTR, but not PDBREF was specified,
+otherwise must not appear. It contains the following group of variables:
+
+(THETA(i),i=3,NRES) - the virtual-bond valence angles THETA
+(PHI(i),i=4,NRES) - the virtual-bond dihedral angles GAMMA
+(ALPH(i),i=2,NRES-1)- the ALPHA polar angles of consecutive side chains
+(OMEG(i),i=2,NRES-1)- the BETA polar angles of consecutive side chains.
+
+ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
+is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
+CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle gamma.
+
+8.1.15 Internal coordinates of the initial conformation (free format;
+---------------------------------------------------------------------
+ subroutine READ_ANGLES)
+ -----------------------
+
+This part of the data is present, if RAND_CONF, MULTCONF, THREAD, or PDBSTART
+were not specified, otherwise must not appear. This input is as in section 10.
+
+8.1.15.1 File name with internal coordinates of the conformations to be processed
+---------------------------------------------------------------------------------
+ (text format; subroutine MOLREAD)
+ ---------------------------------
+
+This data is present only, if MULTCONF was specified. It contains the name of
+the file with the internal coordinates. Up to 64 characters are allowed.
+The structure of the file is that of the *.int file produced by UNRES/CSA.
+See section "The structure of the INT files" for details.
+
+8.1.16 Control data for energy map construction (data lists; subroutine MAP_READ)
+---------------------------------------------------------------------------------
+
+These data lists appear, if NMAP=n was specified, where n is the number of
+variables that will be grid-searched. One list is per one variable or a
+group of variables set equal (see below):
+
+PHI - the variable is a virtual-bond dihedral angle gamma
+THE - the variable is a virtual-bond angle theta
+ALP - the variable is a side-chain polar angle alpha
+OME - the variable is a side-chain polar angle beta
+
+RES1=number (integer)
+RES2=number (integer)
+
+The range of residues for which the values will be set; all these variables
+will be set at the same value. It is required that RES2 > RES1.
+
+FROM=angle (real)
+TO=angle (real)
+
+Lower and upper limit of scanning in grid search (in degrees)
+
+NSTEP=number (integer)
+
+Number of steps in scanning along this variable/group of variables.
+
+8.2. Input coordinate files
+---------------------------
+
+At present, geometry can be input either from the external files in the PDB
+format (with the PDBSTART option) or multiple conformations can be read
+as virtual-bond-valence and virtual-bond dihedral angles when the MULTCONF
+option is used (the latter, however, implies using standard virtual-bond
+lengths as initial values). The structure of internal-coordinate files
+is the same as that of output internal-coordinate files described in section
+9.1.1.
+
+8.3. Other input files
+----------------------
+
+CSA parameters can optionally be read in free format from file INPUT.CSA.in
+(see section 8.1.4). When a CSA run is restarted, the CSA-specific output files
+also serve as input files. INPUT is the prefix of input and output files
+as explained in section 6.
+
+Restart files for MD and REMD simulations. They are read when the keyword
+RESTART appears on the MD/REMD data group (section 8.1.6).
+
+8. OUTPUT FILES
+---------------
+
+UNRES "main" output files (INPUT.out_${POT}[processor]) are log files from
+a run. They contain the information of the molecule, force field, calculation
+type, control parameters, etc.; however, not the structures produced during
+the run or their energies except single-point energy evaluation and
+minimization-related runs. The structural information is included in
+coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat),
+respectively; these files are further processed by other programs (WHAM,
+CLUSTER) or can be viewed by molecular viewers (pdb or mol2 files).
+
+9.1. Coordinate files
+---------------------
+
+9.1.1. The internal coordinate (INT) file
+------------------------------------------
+
+
+This file contains the internal coordinates of the conformations produced
+by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so
+only the angular variables are provided (see ref
+
+IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)
+(I5,F12.5,I2,9(1X,2I3))
+
+IT - the number of the conformation
+ENER - total energy
+NSS - the number of disulfide bridges
+(IHPB(I),JHPB(I),I=1,NSS) - the positions of the pairs of half-cystines
+forming the bridges. If NSS>9, the remaining pairs are written in the
+following lines in the (3X,11(1X,2I3)) format.
+
+(THETA(I),I=3,NRES)
+(8F10.4)
+
+The virtual-bond angles THETA (in degrees)
+
+(PHI(I),I=4,NRES)
+(8F10.4)
+
+The virtual-bond dihedral angles GAMMA (in degrees)
+
+(ALPH(I),I=2,NRES-1)
+(OMEG(I),I=2,NRES-1)
+(8F10.4)
+
+The polar angles ALPHA and BETA of the side-chain centers (in degrees).
+
+9.1.2. The plain Cartesian coordinate (X) files (subroutine CARTOUT)
+--------------------------------------------------------------------
+
+This file contains the Cartesian coordinates of the alpha-carbon and
+side-chain-center coordinates. All conformations from an MD/MREMD
+trajectory are collated to a single file. The structure of each
+conformation's record is as follows:
+
+1st line: time,potE,uconst,t_bath,nss,(ihpb(j),jhpb(j),j=1,nss),
+nrestr,(qfrag(i),i=1,nfrag),(qpair(i),i=1,npair),
+(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
+
+time: MD time (in "molecular time units"; 1 mtu = 4.89 fs),
+potE: potential energy,
+uconst: restraint energy corresponding to restraints on Q and backbone geometry,
+(see section ??),
+t_bath: thermostat temperature,
+nss: number of disulfide bonds,
+ihpb(j), jhpb(j): the numbers of linked cystines for jth disulfide bond,
+nrestr: number of restraints on q and local geometry,
+qfrag(i): q value for ith fragment,
+qpair(i): q value for ith pair,
+utheta(i): sum of squares of the differences between the theta angles
+ of the current conformation from those of the experimental conformation,
+ugamma(i): sum of squares of the differences beaten the gamma angles
+ of the current conformation from those of the experimental conformation,
+uscdiff(i): sum of squares of the differences between the Cartesian difference
+ of the unit vector of the Calpha-SC axis of the current conformation from
+ those of the experimental conformation.
+
+Next lines: Cartesian coordinates of the Calpha atoms (including dummy atoms)
+(sequentially, 10 coordinates per line)
+Next lines: Cartesian coordinates of the SC atoms (including glycines and
+dummy atoms) (sequentially, 10 coordinates per line)
+
+9.1.3. The compressed Cartesian coordinate (CX) files
+-----------------------------------------------------
+
+These files are compressed binary files (extension cx). For each conformation,
+the items are written in the same order as specified in section 9.1.2. For
+MREMD runs, if TRAJ1FILE is specified on MREMD record (see section 8.1.6),
+snapshots from all trajectories are written every time the coordinates
+are dumped. Thus, the file contains snapshot 1 from trajectory 1, ...,
+snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.
+
+The compressed cx files can be converted to pdb file by using the xdrf2pdb
+auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple
+trajectory files from MREMD runs generated by using the TRAJ1FILE option).
+The multiple-trajectory cx files are also input files for the auxiliary
+WHAM program.
+
+9.1.4. The Brookhaven Protein Data Bank format (PDB) files (subroutine PDBOUT)
+------------------------------------------------------------------------------
+
+These files are written in PDB standard (see. e.g.,
+ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf).
+The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+The Calpha (marked CA) and SC (marked CB) coordinates are output. The CONECT
+records specify the Calpha...Calpha and Calpha...SC virtual bonds. Secondary
+structure is detected based on peptide-group contacts, as specified in
+ref 12. Dummy residues are omitted from the output. If the program has
+multiple-chain function, the presence of a dummy residue in a sequence
+starts a new chain, which is assigned the next alphabet letter as ID, and
+residue numbering is started over.
+
+9.1.5. The SYBYLL (MOL2) files
+------------------------------
+
+See the description of mol2 format (e.g.,
+http://tripos.com/data/support/mol2.pdf). Similar remarks apply as for
+the PDB format (section 9.1.4).
+
+9.2. The summary (STAT) file
+----------------------------
+
+9.2.1. Non-MD runs
+------------------
+
+This file contains a short summary of the quantities characterizing the
+conformations produced by UNRES/CSA. It is created for MULTCONF and MCM.
+
+NOUT,EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS,ETOT,RMS,FRAC
+(I5,9(1PE14.5))
+
+NOUT - the number of the conformations
+
+EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS - energy components
+
+ETOT - total energy
+
+RMS - RMS deviation from the reference structure (if REFSTR was specified)
+
+FRAC - fraction of side chain - side chain contacts of the reference
+ structure present in this conformation (if REFSTR was specified)
+
+9.2.2. MD and MREMD runs
+-------------------------
+
+Each line of the stat file generated by MD/MREMD runs contains the following
+items in sequence:
+
+step - the number of the MD step
+
+time - time [unit is MTU (molecular time unit) equal to 48.9 fs]
+
+Ekin - kinetic energy [kcal/mol]
+
+Epot - potential energy [kcal/mol]
+
+Etot - total energy (Ekin+Epot)
+
+H-H0 - the difference between the cureent and initial extended Hamiltionian
+ in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
+
+RMSD - root mean square deviation from the reference structure (only in
+ REFSTR has been specified)
+
+damax - maximum change of acceleration between two MD steps
+
+fracn - fraction of native side-chain concacts (very crude, based on
+ SC-SC distance only)
+
+fracnn - fraction of non-native side-chain contacts
+
+co - contact order
+
+temp - actual temperature [K]
+
+T0 - initial (microcanonical runs) or thermostat (other run types)
+ temperature [K]
+
+Rgyr - radius of gyration based on Calpha coordinates [A]
+
+proc - in MREMD runs the number of the processor (the number of the
+ trajectory less 1); not present for other runs.
+
+For an USAMPL run, the following items follow the above list:
+
+iset - the number of the restraint set
+
+uconst - restraint energy pertaining to q-values
+
+uconst_back - restraint energy pertaining to virtual-backbone restraints
+
+(qfrag(i),i=1,nfrag) - q values of the specified fragments
+
+(qpair(ii2),ii2=1,npair) - q values of the specified pairs of fragments
+
+(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back) - virtual-backbone and
+ side-chain-rotamer restraint energies of the fragments specified
+
+If PRINT_COMPON has been specified, the energy components are printed
+after the items described above.
+
+9.3. CSA-specific output files
+------------------------------
+
+There are several output files from the CSA routine:
+INPUT.CSA.seed, INPUT.CSA.history, INPUT.CSA.bank, INPUT.CSA.bank1,
+INPUT.CSA.rbank INPUT.CSA.alpha, INPUT.CSA.alpha1.
+
+The most informative outfile is INPUT.CSA.history. This file first write down
+the parameters in INPUT.CSA.csa file. Later it shows the energies of random
+minimized conformations in it's generation. After sorting the First_bank
+in energy (ascending order), the energies of the First_bank is re-written here.
+After this the output looks like:
+ 1 0 100 6048.2 1 100-224.124-114.346 202607 100 100
+ 1 0 700 5882.6 2 29-235.019-203.556 1130308 100 100
+ 1 0 1300 5721.5 2 18-242.245-212.138 2028008 100 100
+ 1 0 1900 5564.8 13 54-245.185-218.087 2897988 98 100
+ 1 0 2500 5412.4 13 61-246.214-222.068 3706478 97 100
+ 1 0 3100 5264.2 13 89-248.715-224.939 4514196 96 100
+
+Each line is written between each iteration (just after selection
+of seed conformations) containing following data:
+jlee,icycle,nstep,cutdif,ibmin,ibmax,ebmin,ebmax,nft,iuse,nbank
+ibmin and ibmax lists the index of bank conformations corresponding to the
+lowest and highest energies with ebmin and ebmax.
+nft is the total number of function evaluations so far.
+iuse is the total number of conformations which have not been used as seeds
+prior to calling subroutine select_is which select seeds.
+
+Therefore, in the example shown above, one notes that so far 3100
+minimizations has been performed corresponding to the total of 4514196
+function evaluations. The lowest and highest energy in the Bank is
+-248.715 (#13) and -224.939 (#89), respectively. The number of conformations
+already used as seeds (not including those selected as seeds in this iteration)
+so far is 4 (100-96).
+
+The files INPUT.CSA.bank and INPUT.CSA.rbank contains data of Bank and
+First_bank. For more information on these look subroutines write_bank
+and write_rbank. The file INPUT.CSA.bank is overwritten between each
+iteration whereas Bank is accumulated in INPUT.CSA.bank1 (not for every
+iteration but as specified in the subroutine together.f).
+
+The file INPUT.CSA.seed lists the index of the seed conformations with their
+energies. Files INPUT.CSA.alpha, INPUT.CSA.alpha1 are written only once
+at the beginning of the CSA run. These files contain some arrays used
+in CSA procedure.
+
+10. TECHNICAL SUPPORT CONTACT INFORMATION
+-----------------------------------------
+
+ Dr. Adam Liwo
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: adam@chem.univ.gda.pl
+
+ Dr. Cezary Czaplewski
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: czarek@chem.univ.gda.pl
+
+ Dr. Stanislaw Oldziej
+ Intercollegiate Faculty of Biotechnology
+ University of Gdansk, Medical University of Gdansk
+ ul. Kladki 22, 80-922 Gdansk, Poland
+ phone: +48 58 523 5361
+ fax: +48 58 523 5472
+ e-mail: stan@biotech.ug.gda.pl
+
+ Dr. Jooyoung Lee
+ Korea Institute for Advanced Study
+ 207-43 Cheongnyangni 2-dong, Dongdaemun-gu,
+ Seoul 130-722, Korea
+ phone: +82-2-958-3890
+ fax: +82-2-958-3731
+ email: jlee@kias.re.kr
+
+Prepared by Adam Liwo and Jooyoung Lee, 7/17/99
+Revised by Cezary Czaplewski 1/4/01
+Revised by Cezary Czaplewski and Adam Liwo 8/26/03
+Revised by Cezary Czaplewski and Adam Liwo 11/26/11
+Revised by Adam Liwo 02/19/12
+
projects / unres.git / blobdiff