[e40e335] | 1 | README
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| 2 |
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| 3 | The SMMP package is designed for molecular simulation of linear
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| 4 | proteins within the standard geometry model. The package contains
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| 5 | various modern Monte Carlo algorithms and energy minimization
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| 6 | routines. The energy of the protein can be calculated by exploiting
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| 7 | one of three force fields: ECEPP/2, ECEPP/3 or FLEX. Two subroutines
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| 8 | are included for approximating protein-solvent interaction by means
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| 9 | of calculating the solvent accessible area of atomic groups (either
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| 10 | analytically or in an approximate way). More information on SMMP can
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| 11 | be found in the manual (file `manual.ps'), our papers (F. Eisenmenger,
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| 12 | U.H.E. Hansmann, S. Hayryan and C.K. Hu, [SMMP] A Modern Package for
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| 13 | Protein Simulations, Comp.Phys. Comm. (2001), 138 (2001) 192-212;
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| 14 | [SMMP 1.1] - An Enhanced Open-Source Software Package, submitted), and
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| 15 | on the SMMP homepage: http://www.smmp05.net
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| 16 |
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| 17 | SMMP is offered as open code. We encourage users to re-write code,
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| 18 | or add their own modules, whenever they see the need. For terms of
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| 19 | use of SMMP, please see the manual (manual.pdf) and the license
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| 20 | agreement (license.txt). By viewing or using any part of SMMP you
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| 21 | agree with the terms of the license. Any suggestions for improvement
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| 22 | of the code or reports on bugs are welcome.
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| 23 |
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| 24 | Please send your remarks to:
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| 25 | - Frank Eisenmenger: eisenmenger@fmp-berlin.de
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| 26 | - Ulrich H.E. Hansmann: hansmann@mtu.edu
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| 27 | - Shura Hayryan: shura@phys.sinica.edu.tw
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| 28 | - Chin-Kun Hu: huck@phys.sinica.edu.tw
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| 29 | - Jan H. Meinke j.meinke@fz-juelich.de
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| 30 |
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| 31 |
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| 32 |
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| 33 | 2) INSTALLATION:
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| 34 | After uncompressing and un-tar-ing the SMMP package into a separate
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| 35 | directory, the following files should be in that directory:
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| 36 |
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| 37 | - README This README-file
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| 38 |
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| 39 | - SMMP A sub-directory containing:
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| 40 | - lib.sh2 Library file with ECEPP/2 parameters
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| 41 | - lib.sh3 Library file with ECEPP/3 parameters
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| 42 | - lib.flex Library file with FLEX parameters
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| 43 | - charges File with charges (needed only for FLEX)
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| 44 | - tes.dat File with tesselation points needed for approximating
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| 45 | the solvent accessible surface area of atoms
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| 46 | - doc A sub-directory containing:
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| 47 | - manual.pdf The manual in PDF-format describing the details
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| 48 | of various subroutines and installation of SMMP
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| 49 | - license.txt Ascii-file with the license agreement
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| 50 | - angle_defs.svg Scalable vector graphic of definition of angles
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| 51 | - atom_numbering.svg Scalable vector graphic of numbering of atoms
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| 52 | - dihedral_defs.svg Scalable vector graphic of definition of dihedrals
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| 53 | - Makefile Makefile to build documentation
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| 54 | - manual.lyx Original source of manual
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| 55 | - manual.tex Lyx file converted to tex suitable for pdflatex
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| 56 |
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| 57 | - Makefile Produces the executable file
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| 58 |
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| 59 | - INCL.H Defines global parameters and common-blocks
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| 60 | - INCP.H Defines parameters and common-blocks necessary for reading
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| 61 | PDB-structures
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| 62 | - incl_lund.h Defines parameters and common blocks used with the Lund
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| 63 | force field and BGS
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| 64 |
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| 65 | - init_molecule.f Wrapping function that constructs the start configuration
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| 66 | of a molecule
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| 67 | - init_energy.f Wrapping function that initializes energy parameter
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| 68 | - redseq.f Reads sequence of amino acids (e.g. enkefa.seq)
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| 69 | - redvar.f Reads initial configuration of molecule (e.g. enkefa.var)
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| 70 | - getmol.f Assembles data from libraries
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| 71 | - bldmol.f Builds up the protein atomic coordinates
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| 72 | - addend.f Adds end-groups
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| 73 | - setmvs.f Determines sets of moving atoms for given variables
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| 74 | - mklist.f Compiles lists of interaction partners
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| 75 | - setvar.f Resets variables and rebuilds the molecule
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| 76 | - dihedr.f Returns dihedral angles and valence angles
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| 77 | - difang.f Calculates the difference and the sum of two angles
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| 78 | - nursvr.f Calculates the residue index of a dihedral angle or atom
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| 79 | - redstr.f String input routines
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| 80 | - pdbread.f Reads amino acid sequence and rotein atomic coordinates from
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| 81 | a PDB-file, calculates dihedral angles from PDB coordinates,
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| 82 | and builds index field that relates PDB-atoms to SMMP atoms
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| 83 |
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| 84 | - energy.f Wrapping function that returns the energy of a current
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| 85 | protein configuration
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| 86 | - enyflx.f Calculates internal energy of molecule with FLEX dataset
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| 87 | - enyshe.f Calculates internal energy of molecule with ECEPP datasets
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| 88 | - enyshe_p.f Parallel version of enyshe.f
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| 89 | - enylun.f Calculates energy of molecule using the Lund force field
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| 90 | - enysol.f Calculates solvation energy of molecule using solvent
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| 91 | accessible area method (fast, but approximate calculation)
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| 92 | - enysol_p.f Parallel version of enysol.f
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| 93 | - esolan.f Calculates solvation energy of molecule using solvent
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| 94 | accessible area method (analytic, but slow calculation)
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| 95 | - eninteract.f Calculates interaction term for multi-molecule simulations
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| 96 | based on ECEPP.
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| 97 | - enyreg.f Calculates a constraint energy needed for regularizing
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| 98 | PDB-structures
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| 99 | - eyabgs.f Calculates correction term introduced by R. A. Abagyan
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| 100 | et al.
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| 101 |
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| 102 | - gradient.f Wrapping function that returns the energy gradient vs.
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| 103 | dihedral angles for a protein configuration
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| 104 | - opeflx.f Calculates internal energy and partial derivatives vs.
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| 105 | dihedral angles for FLEX dataset
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| 106 | - opeshe.f Calculates internal energy and partial derivatives vs.
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| 107 | dihedral angles for ECEPP datasets
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| 108 | - opesol.f Calculates analytically the partial derivatives vs.
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| 109 | dihedral angles of the solvation energy
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| 110 | - opereg.f Calculates the partial derivatives vs. diheadral angles
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| 111 | of the constraint energy term during regularization
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| 112 |
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| 113 |
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| 114 | - main.f Main program
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| 115 | - regul.f Regularization of PDB-structure into SMMP geometry
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| 116 | - anneal.f For simulated annealing run
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| 117 | - canon.f For canonical Monte Carlo run
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| 118 | - minim.f For minimization of protein potential energy
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| 119 | - mulcan_par.f Calculates multicanonical weights
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| 120 | - mulcan_sim.f For multicanonical simulation run
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| 121 | - mulcan_par_mod.f90 Combines the previous two files in a Fortran module.
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| 122 | - partem_s.f For parallel tempering run on a single-processor machine
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| 123 | - partem_p.f For parallel tempering run on a multiple-processor machine
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| 124 | - main_p.f Replaces `main.f' on multiple-processor machine in
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| 125 | parallel tempering runs.
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| 126 | - main_bgl_p.f Version of main_p.f optimized for use with IBM BlueGene/L
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| 127 |
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| 128 | - metropolis.f Performs Metropolis updates
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| 129 | - bgs.f Biased Gaussian step.
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| 130 | - minqsn.f Minimization by quasi-Newton method using BFGS-formula
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| 131 | - mincjg.f Minimization by conjugate gradient method
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| 132 | - outvar.f Output of the current conformation (dihedral angles)
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| 133 | - contacts.f Calculates van der Waals contacts
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| 134 | - cnteny.f Calculates atomic contact energy and prints bad contacts
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| 135 | - hbond.f Calculates number of hydrogen bonds in a configuration
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| 136 | - helix.f Measures the number of residues which are part of helix or
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| 137 | beta-sheet
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| 138 | - outpdb.f Output of current configuartion in PDB-format
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| 139 | - rgyr.f Measures the radius-of-gyration and end-to-end distance in
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| 140 | molecule
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| 141 | - zimmer.f Expresses given configuration in Zimmerman code
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| 142 | - rmsdfun.f Calculates root-mean-square deviation between current
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| 143 | SMMP configuration and a reference structure.
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| 144 |
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| 145 | - twister.f Mersenne-Twister random number generator
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| 146 | - utilties.f Somer helper function for simulations on multiple processors.
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| 147 |
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| 148 | - smmp.pyf Interface of the Python bindings
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| 149 |
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| 150 | - universe.py Python package that provides access to global properties
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| 151 | of the system.
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| 152 | - protein.py Python package representing atoms, amino acids, and proteins
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| 153 | - algorithms.py Some basic algorithms using the Python bindings.
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| 154 | - main.py Main program in Python
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| 155 |
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| 156 | - rmexclpoint.py Utility script to build the Python binding
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| 157 | - restoreexclpoint.py Utility script to build the Python binding
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| 158 |
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| 159 | - temperatures Sample temperature file with 32 temperatures.
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| 160 |
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| 161 | - EXAMPLES A sub-directory containing:
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| 162 | - enkefa.seq Example sequence file
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| 163 | - enkefa.var Example configuration file
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| 164 | - enkefa.ann Example configuration filea for simulated annealing run
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| 165 | - enkefa.ref Example contact matrix file
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| 166 | - abeta.seq Sequence file for Abeta_16-22
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| 167 | - abeta.var Configuration file with global coordinates
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| 168 | - abeta.ref Dummy contact matrix
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| 169 | - 1bdd.pdb PDB file of protein A for regularization.
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| 170 | - 1bdd.ref Contact matrix of protein A
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| 171 | - 1bdd.seq Sequence file of protein A
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| 172 | - 1bdd.var Sampe configuration of protein A
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| 173 | - temperatures Example temperature file for parallel_tempering_s
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| 174 | - temperatures_abeta Example temperature file for parallel_tempering
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| 175 | - smmp.cmd Example shell-script to run smmp
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| 176 |
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| 177 | - Makefile Makefile for building the examples.
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| 178 |
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| 179 | - annealing.f Example for running simulated annealing
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| 180 | - minimization.f Example for a minimization
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| 181 | - multicanonical.f Example for calculating parameters for a multi canonical
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| 182 | simulation.
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| 183 | - parallel_tempering_p.f Example for parallel tempering on a cluster
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| 184 | - parallel_tempering_s.f Example for parallel tempering on a single node
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| 185 | - partem_p.f Parallel tempering routine used with parallel_tempering_p.f
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| 186 | The output is different from the default implementation.
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| 187 | - regularization.f Example for regularizing protein A (1bdd)
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| 188 |
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| 189 | - Python A sub-directory containing some examples that use the Python
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| 190 | bindings.
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| 191 |
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| 192 | - annealing.py Python version of the annealing example
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| 193 | - minimization.py Python version of the minimization example
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| 194 | - muca.py Python version for calculating the parameters for a
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| 195 | multi-canonical simulation.
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| 196 | - regularization.py Python version of regularization example
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| 197 | - gui_example.py Example for building a graphical user interface for SMMP
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| 198 | - best.pml A PyMol script for rendering best.pdb
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| 199 |
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| 200 | - scripts A sub-directory containing some useful scripts:
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| 201 | - README Short description of the scripts
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| 202 | - atomprops.py Lists the properties of all atoms in a protein
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| 203 | - var2pdb.py Takes a sequence and a var file and builds a PDB from it.
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| 204 |
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| 205 | The whole SMMP package is written in standard FORTRAN language.
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| 206 | We have been exploiting it under pgif, ifort, gfortran, and xlf.
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| 207 | It should be possible to compile the code with any contemporary fortran
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| 208 | compilers. There are no machine dependent routines included in SMMP.
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| 209 | Common blocks and limiting parameters are gathered in special files
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| 210 | ``INCL.H'' and ``INCP.H'' which are attached to the modules through
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| 211 | an `include' statement. In order to install SMMP the user needs to edit the
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| 212 | `Makefile' and specify the compiler and compiler options which he will use.
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| 213 | Executing the `make' command will finish installation of SMMP. For compiling
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| 214 | the parallel version use `make parallel'. The command `make doc' build the
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| 215 | documentation and `make pybind' build the Python bindings if f2py is installed.
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| 216 |
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| 217 |
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| 218 |
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| 219 | 3) HOW TO RUN SMMP:
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| 220 | SMMP does not include an interpretor of user defined commands.
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| 221 | The preparation of a simulation must be done in the 'main' module
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| 222 | After changes of SMMP has to be re-compiled.
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| 223 |
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| 224 | Alternatively, you can use the Python bindings, which allow for interactive
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| 225 | simulations.
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| 226 |
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| 227 | The residues which can be used with each parameter set are described in
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| 228 | files `lib.sh2', 'lib.sh3' and 'lib.flx', respectively. The file 'charges'
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| 229 | is needed for N- and C-terminal residues with FLEX parameters. The
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| 230 | directory with these 3 files should be given in string 'libdir', which
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| 231 | is assigned in module 'main' or 'pmain'.
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| 232 |
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| 233 | SMMP requires as input a file that specifies the sequence of residues
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| 234 | in a protein. This sequence can be read either from a PDB-file (the
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| 235 | standard format in which protein structures are deposited in the
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| 236 | Protein Data Bank) or from a special sequence file. If the sequence
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| 237 | is read from a sequence file its first line must start with a '#' and
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| 238 | may (or may not) contain the name for the molecule. The residues in the
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| 239 | following lines should be named as in the libraries (not case-
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| 240 | sensitive). Residue names should be separated by at least one space.
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| 241 | An example file ("enkefa.seq") is provided in the sub-directory EXAMPLES.
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| 242 |
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| 243 | The initial values for internal variables, i.e. dihedral angles for single
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| 244 | bonds, can be calculated either from the atomic coordinates of the PDB-file,
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| 245 | or (if the sequence is read from a sequence file) may be provided in a
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| 246 | SECOND INPUT file. If this file is not given (or the name of a non-existing
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| 247 | file is entered), all variables retain their values given in the libraries.
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| 248 | The example file ("enkefa.var") which is provided in the subdirectory
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| 249 | EXAMPLES demonstrates the syntax that has to be used:
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| 250 |
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| 251 | residue(s) : variable(s) : value
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| 252 |
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| 253 | In the first field the RESIDUE is selected through an {\it INTEGER}
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| 254 | number which marks the position of that RESIDUE in the amino acid sequence.
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| 255 | The second field lists a string with the name of the VARIABLE, i.e. names
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| 256 | the specific dihedral angle. The last field lists the value (a {\it REAL}
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| 257 | number) for the VARIABLE and is mandatory. Missing fields are interpreted
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| 258 | as 'for all'. Spaces are not significant and are ignored. Empty lines or
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| 259 | or lines containing '#' are ignored. A line containing '&' assigns FIXED
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| 260 | variable(s), i.e. they will be set to the given value, but will NOT be
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| 261 | varied during subsequent changes of the protein configuration.
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| 262 |
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| 263 |
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| 264 |
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| 265 | The following steps summarize how to run SMMP:
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| 266 |
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| 267 | - Assign to the character variable 'libdir' the path to the directory
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| 268 | containing the standard amino acid residue libraries and the file 'charges'.
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| 269 |
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| 270 | - Select the force field and solvation model by setting the four
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| 271 | 'sh2', 'epsd' and 'itysol', 'ientyp' to their appropriate values:
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| 272 | * ientyp : 0 => ECEPP2 or ECEPP3 depending on the value of sh2
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| 273 | 1 => FLEX
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| 274 | 2 => Lund force field
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| 275 | 3 => ECEPP with Abagyan corrections
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| 276 | * sh2 =.TRUE. : ECEPP/2 potential, sh2=.FALSE.: ECEPP/3
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| 277 | (Note that the variable `flex' has to be set to .FALSE.)
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| 278 | * epsd=.TRUE. : Distant dependent epsilon(r)
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| 279 | epsd=.FALSE.: epsilon=2
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| 280 | * itysol = 0 : Gas phase;
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| 281 | itysol > 0 : approximation of protein-solvent interactions by means
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| 282 | of a solvent accessible surface area approach with
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| 283 | stochastic estimation of the accessible area.
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| 284 | itysol < 0 : same as above, but the accessible area is calculated
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| 285 | analytically (much SLOWER than itysol > 0).
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| 286 |
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| 287 | - Choose a N-terminal and C-terminal group by setting 'grpn' and 'grpc'
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| 288 | to approbriate values.
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| 289 |
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| 290 | - Choose how the initial input is read in:
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| 291 | * iabin = 0 : read from PDB-file
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| 292 | * iabin = 1 : read from sequence (and configuration) file
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| 293 |
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| 294 | - Enter the names of the corresponding file(s). In the example
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| 295 | version of the 'main' module this is done through interactive dialog
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| 296 | but the user can easily just assign the corresponding names to the
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| 297 | character variables 'seqfil' and 'varfil' in the subroutine
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| 298 | 'init_molecule'.
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| 299 |
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| 300 | - At this point the program is ready for calling the simulation
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| 301 | subroutines. In the provided version the energy minimization
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| 302 | subroutine is called through 'call minim'. A detailed description
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| 303 | of this and other simulation subroutines can be found in the
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| 304 | manual (file manual.ps). Normally the simulation subroutines
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| 305 | write data in output files, but one can also put output routines
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| 306 | such as `outpdb' in 'main'. The minimal output (written into
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| 307 | standard output) is the name of the sequence file (extension .seq),
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| 308 | name of configuration file (extension .var), and for each residue
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| 309 | a list of dihedral angles together with their initial values.
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| 310 |
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| 311 | - For parallel tempering jobs on on a multiprocessor system one has
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| 312 | to replace 'main' by 'main_p'. The above protocol still applies.
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| 313 |
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| 314 |
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| 315 | 4) LIMITATIONS:
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| 316 | All parameters which limit the usage of SMMP are stored in the
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| 317 | file ``INCL.H''. The most important ones are listed below.
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| 318 |
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| 319 | mxml=10 max. number of molecules
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| 320 | mxrs=500 max. total number of residues
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| 321 | mxat=10000 max. total number of atoms
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| 322 | mxbd=3 max. number of bonds to following atoms
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| 323 | mxvr=mxrs*5 max. number of local variables
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| 324 | mxms=mxvr*3 max. total number of moving sets
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| 325 | mxvw=mxat*4 max. number of vwd domains
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| 326 | mx14=mxat*4 max. number of '1-4' partners
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| 327 | mxath = 100 max. number of atoms in help-arrays
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| 328 | mxvrh=mxath max. number of variables in help
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| 329 | mxtyat=18 max. number of energetic atom-types
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| 330 | mxhbdo=4 max. types of Hydrogens as donors in HB
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| 331 | mxhbac=6 max. types of atoms as acceptors in HB
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| 332 | mxtyto=19 max. number of types of torsional potentials
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| 333 | nrsty=35 max. number of residue types
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| 334 | mxtysol=9 the number of solvation parameters sets
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| 335 |
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| 336 | Note also the following restrictions in the current version of SMMP:
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| 337 | - A single amino acid residue can not be simulated with FLEX potential.
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| 338 | - A protein must not start with a prolin residue.
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| 339 |
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| 340 |
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| 341 | 5) EXAMPLE:
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| 342 | Proper installation of SMMP can be tested by running the following
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| 343 | example. After compilation of the program package (with `make'
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| 344 | command using the provided `Makefile') and runing SMMP by typing
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| 345 | ./smmp, SMMP will minimize the ECEPP/3 energy of the Met-enkephalin
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| 346 | configuration in `EXAMPLES/enkefa.var'.
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| 347 | -----------------------------------------------------------------------
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| 348 | |NOTE: If the program doesn't start but only shows the error message |
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| 349 | |"Killed", you probably don't have enough memory available. You can |
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| 350 | |reduce the memory requirement by setting lower limits for mxrs |
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| 351 | |(line 10) and mxat (line 11) in the file INCL.H. Setting mxrs=10 and |
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| 352 | |mxat=1300 will still run all the examples. |
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| 353 | -----------------------------------------------------------------------
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| 354 | Running the program leads to the following output:
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| 355 |
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| 356 | ------------------------------------------------------------ enkefa.out
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| 357 |
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| 358 | file with SEQUENCE:
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| 359 | ./EXAMPLES/enkefa.seq
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| 360 |
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| 361 | file with VARIABLES: ./EXAMPLES/enkefa.var
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| 362 |
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| 363 | redvar> Met-Enkephalin: residue 1 Tyr : x1 set -172.590
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| 364 | redvar> Met-Enkephalin: residue 1 Tyr : x2 set 78.710
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| 365 | redvar> Met-Enkephalin: residue 1 Tyr : x6 set -165.880
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| 366 | redvar> Met-Enkephalin: residue 1 Tyr : phi set -86.240
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| 367 | redvar> Met-Enkephalin: residue 2 Gly : psi set 156.180
|
---|
| 368 | redvar> Met-Enkephalin: residue 2 Gly : omg set -180.000
|
---|
| 369 | redvar> Met-Enkephalin: residue 2 Gly : phi set -154.530
|
---|
| 370 | redvar> Met-Enkephalin: residue 3 Gly : psi set 83.640
|
---|
| 371 | redvar> Met-Enkephalin: residue 3 Gly : omg set 180.000
|
---|
| 372 | redvar> Met-Enkephalin: residue 3 Gly : phi set 83.660
|
---|
| 373 | redvar> Met-Enkephalin: residue 4 Phe : psi set -73.860
|
---|
| 374 | redvar> Met-Enkephalin: residue 4 Phe : omg set -180.000
|
---|
| 375 | redvar> Met-Enkephalin: residue 4 Phe : x1 set 58.790
|
---|
| 376 | redvar> Met-Enkephalin: residue 4 Phe : x2 set 94.600
|
---|
| 377 | redvar> Met-Enkephalin: residue 4 Phe : phi set -137.040
|
---|
| 378 | redvar> Met-Enkephalin: residue 5 Met : psi set 19.330
|
---|
| 379 | redvar> Met-Enkephalin: residue 5 Met : omg set -180.000
|
---|
| 380 | redvar> Met-Enkephalin: residue 5 Met : x1 set 52.760
|
---|
| 381 | redvar> Met-Enkephalin: residue 5 Met : x2 set 175.280
|
---|
| 382 | redvar> Met-Enkephalin: residue 5 Met : x3 set -179.830
|
---|
| 383 | redvar> Met-Enkephalin: residue 5 Met : x4 set -58.570
|
---|
| 384 | redvar> Met-Enkephalin: residue 5 Met : phi set -163.630
|
---|
| 385 | redvar> Met-Enkephalin: residue 5 Met : pst set 160.450
|
---|
| 386 | redvar> Met-Enkephalin: residue 5 Met : omt set 180.000
|
---|
| 387 |
|
---|
| 388 |
|
---|
| 389 | Energy BEFORE minimization:
|
---|
| 390 |
|
---|
| 391 | Total: 0.10354E+04
|
---|
| 392 | Coulomb: 0.1991E+02 Lennard-Jones: 0.1142E+03 HB: 0.9008E+03
|
---|
| 393 | Variables: 0.4511E+00 Solvatation: 0.0000E+00
|
---|
| 394 |
|
---|
| 395 | Step 1: energy 0.489976E+05 ( 0.867243E+13 )
|
---|
| 396 | Step 2: energy 0.108241E+03 ( 0.964364E+07 )
|
---|
| 397 | Step 3: energy -0.632755E+00 ( 0.498256E+04 )
|
---|
| 398 | Step 4: energy -0.739539E+01 ( 0.109979E+05 )
|
---|
| 399 | Step 5: energy 0.517957E+03 ( 0.678892E+09 )
|
---|
| 400 | Step 6: energy -0.767774E+01 ( 0.143880E+05 )
|
---|
| 401 | Step 7: energy -0.818570E+01 ( 0.100364E+05 )
|
---|
| 402 | Step 8: energy -0.938401E+01 ( 0.172508E+04 )
|
---|
| 403 | Step 9: energy -0.109799E+02 ( 0.105718E+04 )
|
---|
| 404 | Step 10: energy -0.116244E+02 ( 0.580821E+03 )
|
---|
| 405 | Step 11: energy -0.116969E+02 ( 0.145676E+04 )
|
---|
| 406 | Step 12: energy -0.118569E+02 ( 0.856882E+03 )
|
---|
| 407 | Step 13: energy -0.119576E+02 ( 0.521381E+03 )
|
---|
| 408 | Step 14: energy -0.120897E+02 ( 0.398602E+03 )
|
---|
| 409 | Step 15: energy -0.121476E+02 ( 0.222201E+03 )
|
---|
| 410 | Step 16: energy -0.121804E+02 ( 0.242613E+03 )
|
---|
| 411 | Step 17: energy -0.121975E+02 ( 0.237765E+03 )
|
---|
| 412 | Step 18: energy -0.122092E+02 ( 0.217435E+03 )
|
---|
| 413 | Step 19: energy -0.122177E+02 ( 0.198576E+03 )
|
---|
| 414 | Step 20: energy -0.122259E+02 ( 0.181726E+03 )
|
---|
| 415 | Step 21: energy -0.122298E+02 ( 0.178796E+03 )
|
---|
| 416 | Step 22: energy -0.122318E+02 ( 0.178968E+03 )
|
---|
| 417 | Step 23: energy -0.122352E+02 ( 0.181503E+03 )
|
---|
| 418 | Step 24: energy -0.122407E+02 ( 0.184272E+03 )
|
---|
| 419 | Step 25: energy -0.122499E+02 ( 0.186336E+03 )
|
---|
| 420 | Step 26: energy -0.122634E+02 ( 0.183760E+03 )
|
---|
| 421 | Step 27: energy -0.122776E+02 ( 0.171223E+03 )
|
---|
| 422 | Step 28: energy -0.122929E+02 ( 0.148718E+03 )
|
---|
| 423 | Step 29: energy -0.123122E+02 ( 0.119336E+03 )
|
---|
| 424 | Step 30: energy -0.123348E+02 ( 0.847677E+02 )
|
---|
| 425 | Step 31: energy -0.123572E+02 ( 0.434069E+02 )
|
---|
| 426 | Step 32: energy -0.123733E+02 ( 0.176053E+02 )
|
---|
| 427 | Step 33: energy -0.123858E+02 ( 0.941361E+01 )
|
---|
| 428 | Step 34: energy -0.123956E+02 ( 0.739923E+01 )
|
---|
| 429 | Step 35: energy -0.124014E+02 ( 0.513793E+01 )
|
---|
| 430 | Step 36: energy -0.124049E+02 ( 0.385630E+01 )
|
---|
| 431 | Step 37: energy -0.124083E+02 ( 0.416421E+01 )
|
---|
| 432 | Step 38: energy -0.124122E+02 ( 0.530410E+01 )
|
---|
| 433 | Step 39: energy -0.124159E+02 ( 0.493920E+01 )
|
---|
| 434 | Step 40: energy -0.124184E+02 ( 0.306992E+01 )
|
---|
| 435 | Step 41: energy -0.124201E+02 ( 0.174747E+01 )
|
---|
| 436 | Step 42: energy -0.124216E+02 ( 0.110719E+01 )
|
---|
| 437 | Step 43: energy -0.124231E+02 ( 0.793785E+00 )
|
---|
| 438 | Step 44: energy -0.124242E+02 ( 0.585080E+00 )
|
---|
| 439 | Step 45: energy -0.124249E+02 ( 0.454481E+00 )
|
---|
| 440 | Step 46: energy -0.124257E+02 ( 0.491193E+00 )
|
---|
| 441 | Step 47: energy -0.124268E+02 ( 0.498392E+00 )
|
---|
| 442 | Step 48: energy -0.124277E+02 ( 0.297774E+00 )
|
---|
| 443 | Step 49: energy -0.124281E+02 ( 0.987143E-01 )
|
---|
| 444 | Step 50: energy -0.124282E+02 ( 0.562089E-01 )
|
---|
| 445 | Step 51: energy -0.124283E+02 ( 0.472681E-01 )
|
---|
| 446 | Step 52: energy -0.124283E+02 ( 0.360471E-01 )
|
---|
| 447 | Step 53: energy -0.124284E+02 ( 0.149691E-01 )
|
---|
| 448 | Step 54: energy -0.124285E+02 ( 0.376934E-02 )
|
---|
| 449 | Step 55: energy -0.124285E+02 ( 0.243872E-02 )
|
---|
| 450 | Step 56: energy -0.124285E+02 ( 0.253572E-02 )
|
---|
| 451 | Step 57: energy -0.124285E+02 ( 0.176076E-02 )
|
---|
| 452 | Step 58: energy -0.124285E+02 ( 0.952400E-03 )
|
---|
| 453 | Step 59: energy -0.124285E+02 ( 0.889573E-03 )
|
---|
| 454 | Step 60: energy -0.124285E+02 ( 0.747233E-03 )
|
---|
| 455 | Step 61: energy -0.124285E+02 ( 0.417036E-03 )
|
---|
| 456 | Step 62: energy -0.124285E+02 ( 0.307630E-03 )
|
---|
| 457 | Step 63: energy -0.124285E+02 ( 0.474529E-03 )
|
---|
| 458 | Step 64: energy -0.124285E+02 ( 0.506211E-03 )
|
---|
| 459 | Step 65: energy -0.124285E+02 ( 0.298789E-03 )
|
---|
| 460 | Step 66: energy -0.124285E+02 ( 0.125304E-03 )
|
---|
| 461 | Step 67: energy -0.124285E+02 ( 0.153436E-03 )
|
---|
| 462 | Step 68: energy -0.124285E+02 ( 0.132386E-03 )
|
---|
| 463 | Step 69: energy -0.124285E+02 ( 0.661655E-04 )
|
---|
| 464 | Step 70: energy -0.124285E+02 ( 0.194869E-04 )
|
---|
| 465 | Step 71: energy -0.124285E+02 ( 0.120524E-04 )
|
---|
| 466 | Step 72: energy -0.124285E+02 ( 0.641640E-05 )
|
---|
| 467 | Step 73: energy -0.124285E+02 ( 0.182141E-05 )
|
---|
| 468 | Step 74: energy -0.124285E+02 ( 0.219308E-05 )
|
---|
| 469 | Step 75: energy -0.124285E+02 ( 0.348349E-05 )
|
---|
| 470 | Step 76: energy -0.124285E+02 ( 0.166901E-05 )
|
---|
| 471 | Step 77: energy -0.124285E+02 ( 0.177102E-06 )
|
---|
| 472 | Step 78: energy -0.124285E+02 ( 0.663522E-08 )
|
---|
| 473 | Step 79: energy -0.124285E+02 ( 0.210693E-08 )
|
---|
| 474 | Step 80: energy -0.124285E+02 ( 0.370905E-08 )
|
---|
| 475 | Step 81: energy -0.124285E+02 ( 0.324300E-08 )
|
---|
| 476 | Step 82: energy -0.124285E+02 ( 0.777363E-09 )
|
---|
| 477 | Step 83: energy -0.124285E+02 ( 0.443359E-10 )
|
---|
| 478 | Step 84: energy -0.124285E+02 ( 0.322695E-11 )
|
---|
| 479 | Step 85: energy -0.124285E+02 ( 0.443359E-10 )
|
---|
| 480 | ---- CONVERGENCE ----
|
---|
| 481 |
|
---|
| 482 | Final energies __________________________________________________
|
---|
| 483 |
|
---|
| 484 | Total: -0.12429E+02
|
---|
| 485 | Coulomb: 0.2143E+02 Lennard-Jones: -0.2923E+02 HB: -0.6706E+01
|
---|
| 486 | Variables: 0.2084E+01 Solvatation: 0.0000E+00
|
---|
| 487 |
|
---|
| 488 | Variables _________________
|
---|
| 489 |
|
---|
| 490 | x1 1 -173.2 ( 0.6)
|
---|
| 491 | x2 1 79.3 ( 0.6)
|
---|
| 492 | x6 1 -166.3 ( 0.5)
|
---|
| 493 | phi 1 -83.1 ( 3.2)
|
---|
| 494 | psi 2 155.8 ( 0.4)
|
---|
| 495 | omg 2 -177.1 ( 2.9)
|
---|
| 496 | phi 2 -154.2 ( 0.3)
|
---|
| 497 | psi 3 85.8 ( 2.2)
|
---|
| 498 | omg 3 168.5 ( 11.5)
|
---|
| 499 | phi 3 83.0 ( 0.7)
|
---|
| 500 | psi 4 -75.0 ( 1.2)
|
---|
| 501 | omg 4 -170.0 ( 10.0)
|
---|
| 502 | x1 4 58.9 ( 0.1)
|
---|
| 503 | x2 4 94.5 ( 0.1)
|
---|
| 504 | phi 4 -136.8 ( 0.2)
|
---|
| 505 | psi 5 19.1 ( 0.2)
|
---|
| 506 | omg 5 -174.1 ( 5.9)
|
---|
| 507 | x1 5 52.9 ( 0.1)
|
---|
| 508 | x2 5 175.3 ( 0.0)
|
---|
| 509 | x3 5 -179.9 ( 0.0)
|
---|
| 510 | x4 5 -58.6 ( 0.0)
|
---|
| 511 | phi 5 -163.4 ( 0.2)
|
---|
| 512 | pst 5 160.8 ( 0.3)
|
---|
| 513 | omt 5 -179.8 ( 0.2)
|
---|
| 514 |
|
---|
| 515 | Gradient ______________________________________________________________
|
---|
| 516 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|
| 517 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|
| 518 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|