+++ /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