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minAmber.pl
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]
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 A 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
<docmark>genrestr.pl</docmark> 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
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 ...