MMTSB
Tool Set Documentation

minAmber.pl

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Usage

usage:   minAmber.pl [options] PDBfile
options: [-par Amberparams]
         [-l [ca|cb|cab|heavy] force refpdb min:max[=...]]
         [-cons [ca|cb|cab|heavy] refpdb min:max[_force][=...]]
         [-log logFile] [-elog energyLogFile]
         [-[no]translate]
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Description

This script is used to minimize a protein structure from a PDB file with Amber. Without any options a 50-step steepest descent minimization is followed by the a conjugate gradient minimization algorithm over 500 steps or until the energy decrease between steps becomes less than 1.0E-5 kcal/mol. With the default protocol the minimization is carried in vacuum (constant dielectric of 1.0) with a 14.0 Å cutoff for non-bonded interactions.

Command-line options are available to change the default protocol, introduce restraints and specify output files.

Minimization parameters can be set with -par followed by key=value pairs. A complete list of parameters is available here. The most relevant options are explained in the following: The number of steps in the final conjugate gradient minimization run is set with minsteps, a different energy tolerance is selected with minetol. The number of steps during the initial steepest descent minimization is changed with sdsteps. The type of dielectric environment can be set as constant with dielec=cdie or distance dependent with dielec=rdie. The value of epsilon can be changed using epsilon. The non-bonded cutoff radius is set with cutoff or switched off completely with nocut. The hsd and hse parameters are available to specify explicitly the protonation site for histidine residues. By default HSD is assumed (protonated at ND1).

By default, the PARAM94 force field is used. Other Amber force fields may be selected with -param. More information on differences between these force fields is available from the Amber web site.

More realistic than constant or distance-dependent dielectrics but less expensive than explicit solvent is an implicit solvent approximation based on a generalized Born (GB) formalism. This function is available with the gb switch of the -par option. It needs to be set to one of the methods implemented in Amber. Possible options are: tc: Tsui & Case, tc6 Tsui & Case (original radii), obc: Onufriev, Bashford, Case, jsb: Jayaram, Sprous, Beveridge, mgb: modified Jayaram, Sprous, Beveridge. Again, more information is available on the Amber web site.

Different types of restraints may be specified to keep parts of the structure near their initial positions or near coordinates from a reference file. This is useful for modeling of fragments or loops in otherwise known structure templates. Atom-based restraints are specified with -cons or -l. -cons requires a list of residue ranges where the restraints should be applied and corresponding force constants. By default all heavy atoms will be restrained to their initial positions. The keywords ca, cb, or cab can be specified to select only C-alpha, C-beta, or C-alpha/C-beta restraints, respectively. If a file name is given, the reference atom positions from this file are used instead of the initial coordinates from the input file.

In loop modeling it is more convenient to specify the residues in the loop rather than the residues outside the loop for which restraints would be requested. The option -l is available to specify a range of residues that are kept flexible, while restraints are generated implicitly for all other residues outside the given residue range(s). The syntax is otherwise similar to -cons. However, only a single force constant can be supplied as an extra argument. The restraints are generated with continuously increasing force constants from the beginning and ends of the loop regions up to the specified force constant in a similar fashion as the force constants generated by genrestr.pl for lattice simulations.

The final structure after minimization is written to standard output if input is read from standard input or to a file name derived from the input file name by adding min. An alternate output file name can be specified with -out.

The options -log and -elog are available to save the complete output from Amber or only the energy values at each printed minimization step, respectively

The location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least AMBERHOME should be set accordingly. Otherwise an attempt is made to locate the Amber binary from the search path and deduce the data directory from the binary location. The current version of this utility expects Amber 7 for full functionality.

A similar script minCHARMM.pl is available for minimizations using CHARMM.

Options

-help 
usage information
-par key=value[,...] 
Amber simulation paramters
-l [ca|cb|cab|heavy] force refpdb min:max[=...] 
restrain residues outside the specified residue range
-cons [ca|cb|cab|heavy] refpdb min
max[_force][=...] : restrain residue within the specified residue range
-log file 
Amber log file
-elog file 
Amber energy log file
-[no]translate 
(do not) translate input PDB structure

Examples

minAmber.pl 1vii.exp.pdb
performs a minimization in vacuum over 500 steps and writes the minimized structure to standard output

ATOM      1  N   MET     1       1.329 -10.663  -3.566  1.00  0.00          
ATOM      2  H1  MET     1       0.602 -11.369  -3.644  1.00  0.00          
ATOM      3  H2  MET     1       1.978 -10.977  -2.851  1.00  0.00          
ATOM      4  H3  MET     1       1.811 -10.563  -4.453  1.00  0.00          
ATOM      5  CA  MET     1       0.704  -9.385  -3.145  1.00  0.00          
ATOM      6  HA  MET     1       1.476  -8.666  -2.865  1.00  0.00          
ATOM      7  CB  MET     1      -0.202  -8.774  -4.234  1.00  0.00          
ATOM      8  HB2 MET     1      -0.870  -9.538  -4.638  1.00  0.00          
ATOM      9  HB3 MET     1      -0.827  -8.013  -3.767  1.00  0.00          
ATOM     10  CG  MET     1       0.565  -8.093  -5.371  1.00  0.00          

...


minAmber.pl -par gb,minsteps=300,minetol=1E-3,nocut -log amber.log -elog ener.log 1vii.exp.pdb
performs minimization of the given PDB structure with Generalize Born-type implicit solvent over 300 steps or until an energy tolerance of 0.001 is reached. Also, effectively no cutoffs are used for non-bonded interactions. In addition to the minimized structure written to standard output, Amber output is written to amber.log and a log of relevant energy terms, extracted from the Amber output, is written to ener.log.

ATOM      1  N   MET     1       1.449  -9.958  -3.767  1.00  0.00          
ATOM      2  H1  MET     1       1.022 -10.874  -3.747  1.00  0.00          
ATOM      3  H2  MET     1       2.156  -9.924  -3.048  1.00  0.00          
ATOM      4  H3  MET     1       1.894  -9.827  -4.664  1.00  0.00          
ATOM      5  CA  MET     1       0.417  -8.916  -3.530  1.00  0.00          
ATOM      6  HA  MET     1       0.903  -7.941  -3.463  1.00  0.00          
ATOM      7  CB  MET     1      -0.619  -8.871  -4.668  1.00  0.00          
ATOM      8  HB2 MET     1      -0.907  -9.891  -4.929  1.00  0.00          
ATOM      9  HB3 MET     1      -1.516  -8.351  -4.326  1.00  0.00          
ATOM     10  CG  MET     1      -0.111  -8.139  -5.917  1.00  0.00          

...


minAmber.pl -par minsteps=300,sdsteps=20,dielec=rdie,epsilon=4.0 -cons ca self 1:36_0.5 -elog ener.log 1vii.exp.pdb
performs a vacuum minimization of the given PDB structure over 300 steps with 20 steps of initial steepest descent minimization. A distance dependent dielectric with epsilon=4 are used. During the minimization C-alpha atoms of all residues (1 through 36) are restrained to their initial position with a force constant of 0.5 kcal/mol. The energies are written out to ener.log.

ATOM      1  N   MET     1       1.449 -10.044  -3.680  1.00  0.00          
ATOM      2  H1  MET     1       1.116 -10.909  -3.281  1.00  0.00          
ATOM      3  H2  MET     1       2.315  -9.784  -3.232  1.00  0.00          
ATOM      4  H3  MET     1       1.602 -10.168  -4.667  1.00  0.00          
ATOM      5  CA  MET     1       0.439  -8.989  -3.463  1.00  0.00          
ATOM      6  HA  MET     1       0.943  -8.030  -3.360  1.00  0.00          
ATOM      7  CB  MET     1      -0.538  -8.893  -4.644  1.00  0.00          
ATOM      8  HB2 MET     1      -0.835  -9.898  -4.947  1.00  0.00          
ATOM      9  HB3 MET     1      -1.438  -8.352  -4.336  1.00  0.00          
ATOM     10  CG  MET     1       0.078  -8.147  -5.833  1.00  0.00          

...


minAmber.pl -par gb,minsteps=1000,cutoff=22 -l ca 1.5 1vii.exp.pdb 10:21 -elog ener.log 1vii.rebuilt.10:21.pdb
minimizes the structure from the input PDB file with Generalized Born implicit solvent using an interaction cutoff of 22 A. C-alpha atoms outside of residues 10 through 21 are restrained to the position in the reference PDB structure 1vii.exp.pdb. This example shows typical usage for fragment modeling where part of the protein structure is modeled against a fixed template structure.

ATOM      1  N   MET     1       1.328 -10.043  -3.927  1.00  0.00          
ATOM      2  H1  MET     1       0.849 -10.935  -3.987  1.00  0.00          
ATOM      3  H2  MET     1       2.016 -10.090  -3.194  1.00  0.00          
ATOM      4  H3  MET     1       1.790  -9.846  -4.803  1.00  0.00          
ATOM      5  CA  MET     1       0.348  -8.959  -3.613  1.00  0.00          
ATOM      6  HA  MET     1       0.870  -8.004  -3.526  1.00  0.00          
ATOM      7  CB  MET     1      -0.738  -8.795  -4.700  1.00  0.00          
ATOM      8  HB2 MET     1      -1.207  -9.761  -4.935  1.00  0.00          
ATOM      9  HB3 MET     1      -1.533  -8.117  -4.349  1.00  0.00          
ATOM     10  CG  MET     1      -0.192  -8.189  -5.997  1.00  0.00          

...