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| File | Date | Author | Commit |
|---|---|---|---|
| VMD_plugins | 2013-02-26 |
Tom Rodgers
|
[9bf1c5] Initial commit |
| misc | 2013-04-24 |
Tom Rodgers
|
[7fff90] Update of covar.f90 |
| plot | 2013-04-24 |
Tom Rodgers
|
[7fff90] Update of covar.f90 |
| sourcecode | 2013-04-24 |
Tom Rodgers
|
[7fff90] Update of covar.f90 |
| README | 2013-04-01 |
Tom Rodgers
|
[fb4d8e] Updates from paper |
| chain.dat | 2013-02-26 |
Tom Rodgers
|
[9bf1c5] Initial commit |
| configure | 2013-02-26 |
Tom Rodgers
|
[9bf1c5] Initial commit |
| resmass.dat | 2013-02-26 |
Tom Rodgers
|
[9bf1c5] Initial commit |
Read Me
DDPT
Quick Install:
1. ./configure
2. make
3. make install (sudo if you have not selected a local path)
4. Enjoy!
This toolbox has been tested with:
gfortran > 4.4.1
ifort > 11.1
Help:
Help for all programs is available by using the -help tag
when running the program. These help messages are listed at
the end of this file.
For problems with the code please contact thomas.rodgers(at)durham.ac.uk
DDPT: A Comprehensive Toolbox for the Analysis of Protein Motion
Copyright (C) Thomas Rodgers and David Burnell 2012
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Please note the use of Trajutils and Foul within this toolbox which hold
their own GNU General Public Licenses. Please see trajutils.f90 and
foul.f90 for these
G E N E N M M
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program produces the Hermitian matrix for a ENM based on the pdb
inputed with -pdb. A matrix.sdijf file is produced which can be
diagonalised using DIAGSTD to calculate the eigenvalues and vectors.
This program also outputs a map of the spring connections, ENM.vmd which
can be viewed using VMD, and a pdb of the Ca atoms only, CAonly.pdb
Usage:
genENM -pdb pdbfile [-c cut-off] [-f force] [-ccust cfile]
[-fcust ffile] [-spcust spfile] [-mass] [-ca]
[-lig1] [-res] [-het] [-hin] [-hine h] [-an p]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-c Input,Opt 12 Cut-off for spring connectivity
-f Input,Opt 1 Spring constant
-ccust Input,Opt Allows custom cutoffs read from cfile
-fcust Input,Opt Allows custom spring constants read
from ffile
-spcust Input,Opt Allows custom springs to be included
-mass Opt Uses actual atom masses
-ca Opt Calculates Ca model only
-lig1 Opt Assigns each residue in the HETATMs one
average point, only works with -het and
-ca flags as well
-res Opt Assigns ca atom the whole residue mass,
only works with -ca flag as well
-het Opt Includes reading HETATM records
-hin Opt Uses Hinsen fitted interactions
-hine Input,Opt Uses Hinsen exponential interactions
instead, h is the decay factor
-an Input,Opt Uses anisotropic interactions instead,
p is the order of the power decay
cfile format:
WRITE(cfile,'(A4,1X,F7.3)') atomname, cutoff
atomname is in pdb format
e.g.
| C 8.000
| N 8.000
ffile format:
WRITE(ffile,'(1X,I4,1X,A1,1X,I4,1X,A1,1X,F8.3)')
res1, chain1, res2, chain2, kij
res is the residue numbers, chain is the chain code.
res2 can be * which means all connections with res1
e.g.
| 34 A 24 A 3.0
| 329 A * B 3.0
N.B. this will only set connections if within cutoff
spfile format:
WRITE(spfile,'(2(1X,I4,1X,A1))') res1, chain1, res2, chain2
res is the residue numbers. chain is the chain associated with res
e.g.
| 34 A 24 B
| 329 C 124 D
N.B. this will only set connections regardless of cutoff
D I A G S T D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal modes for a ENM based on the reduced
Hermitian matrix file, matrix.sdijf, produced from the ENM program.
A matrix.eigenfacs file is produced which can be further analysed using
the programs in this toolbox.
Usage:
diagstd [-i matrix]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.sdijf reduced Hermitian matrix file
D I A G R T B
VERSION 1.0
Written by:
This program calculates the normal modes for a ENM using the rotational
translational block method based on the reduced Hermitian matrix file,
matrix.sdijf, produced from the ENM program.
The ENM can be split by residues, by the secondary structure (SECO) using
the HELIX and SHEET comands in the pdb, or by custom domains (DOMN) read
from input.domain file.
A matrix.eigenfacs file is produced which can be further analysed using
the programs in this toolbox.
Usage:
diagrtb -pdb pdbfile [-i matrix] [-r num] [-str option]
[-mass] [-het] [-e num] [-high] [-eig] [-mat]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file
-i Input,Opt matrix.sdijf Reduced Hermitian matrix file
-r Input,Opt 1 Number of residues per block
-str Input,Opt NONE Substructuring options, NONE, SECO,
or DOMN
-mass Opt Use true atom masses
-res Opt Use atom residue mass
-het Opt Also read HETATM records
-e Input,Opt 56 Number of eigenvectors output
-eig Opt Print eigenvalues for RTBs
-mat Opt Print RTB matrix
-covar Opt Run with covar matrix input
input.domain format:
WRITE('input.domain','(I4,1X,A1,1X,I4,1X,I4)') domb, cdom, doms, dome
atomname is in pdb format
e.g.
| 1 A 10 15
| 2 B 20 30
G N M P R O D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal modes for a GNM based on the pdb
inputed with -pdb. A matrix.eigenfacs file is produced which can be
further analysed using the programs in this toolbox.
This program also outputs a map of the spring connections, GNM.vmd which
can be viewed using VMD, a representation of the pdb in 2d, flat.pdb, and
a pdb of the Ca atoms only, CAonly.pdb.
Usage:
GNM -pdb pdbfile [-c cut-off] [-f force] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-c Input,Opt 12 Cut-off for spring connectivity
-f Input,Opt 1 Spring constant
-het Opt Include HETATM references with flag
F R E Q / E N
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal mode frequencies, output in
mode.frequencies, from an eigenfacs formated file which can be produced
from the included ENM code, GNM code, and the GroAMED packages.
This program also outputs the energy parameters for the normal modes,
output in mode.energy. The value of the partition function, Z; the
full harmonic free energy, G; the Schlitter free energy, Gs; the full
harmanic entropy, S; and the Schlitter entropy, Ss, are given for each
mode.
Usage:
frequency [-i infile] [-t temperature]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs Eigenvector file name
-t Input,Opt 298 Temperature of entropy calculation
-s Input,Opt 1 First eigenvalue included
-e Input,Opt 1000 Last eigenvalue included
N M W I Z W T
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program creates a file suitable for use with the VMD plugin NMWiz,
output as nmwix.nmd, from an eigenfacs formated file which can be
produced from the included ENM code, GNM code, GroNM, GroED, or AmberED
packages. It also requires the matching pdb and the mode.bfactors file
produced with the rms program.
Usage:
w_nmwiz [-i infile] [-pdb pdbfile] [-n numberofmodes]
[-b bfactorfile] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs Eigenvector file
-pdb Input,Opt CAonly.pdb PDB filename
-n Input,Opt 25 Number of modes written
-b Input,Opt mode.bfactors Calculated bfactor file
-het Opt Incudes reading HETATM records with flag
C R O S C O R
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the average residue cross correlation from an
eigenfacs formated file which can be produced from the included ENM
code, GNM code, or the GroAMED packages.
The output file, crosscor.dat can be plotted in gnuplot with the command:
splot "crosscor.dat" using 1:2:3 notitle
Usage:
cross_cor -i infile [-s startvec]
[-e endvec] [-d1] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input First eigenvector file
-s Input,Opt 7 First included eigenvector number
-e Input,Opt 31 Last included eigenvector number
-d1 Opt Allows 1d vectors with flag
-het Opt Incudes reading HETATM records with flag
R M S / C O L
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the RMSD of each of the atoms for each mode,
output in rms.val, from an eigenfacs formated file which can be produced
from the included ENM code, GNM code, or the GroAMED package.
This program also outputs the collectivity of each mode, output in
collectivity.val.
This program also calculates the predicted bfactors and compares them
with the experimental values given in the original pdbfile, output in
mode.bfactors.
Usage:
rms [-i infile] [-pdb pdbfile] [-s startvec]
[-e endvec] [-d1] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs First eigenvector file
-pdb Input,Opt CAonly.pdb pdb file
-s Input,Opt 7 First included eigenvector number
-e Input,Opt 31 Last included eigenvector number
-d1 Opt Allows 1d vectors with flag
-het Opt Incudes reading HETATM records with flag
G R O A M E D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program converts the output from gromacs g_covar, gromacs g_nmeig,
and amber ptraj commands into files that are compatable with this
toolbox. For gromacs, the eigenvec.trr file needs to be converted into a
readable format using gromacs:
gmxdump -f eigenvec.trr > eigenvec.out
This file can then be input using the -i flag.
The average pdb file produced by gromacs is also needed with the original
pdb file that was used. The eigenval.xvg produced by gromacs is also
used.
A matrix.eigenfacs file is outputted with a pdb file of the Ca atoms,
CAonly.pdb
Usage:
GroAMED -i infile -mdpdb mdpdb -pdb originalpdb
[-eigen eigenfile] [-lig ligand] [-nofit] [-ca]
[-mass resmass]
Option Type Value Description
------------------------------------------------------------
-i Input CA ouputfile
-mdpdb Input MD output pdbfile
-pdb Input Original pdb file
-eigen Input,Opt eigenval.xvg Generated eigenvalue file
-lig Input,Opt NONE Name of any ligand included
-nofit Opt Use if no fitting was used in gromacs
-ca Opt Use if only Ca atoms were fit in gromacs
-mass Input,Opt 99.466 Average residue mass for rescaling if
-ca is used
-nm Opt Use normal mode data instead of PCA data
P L O T P D B
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program copies values for each residue into the bfactor position
in a pdb, if Ca only pdb then the values will be assigned to each Ca
atom, if a full pdf then the values will be assigned to each residue. It
adjusts the second chain assuming that the same residue starts, the
offset can be adjusted with -o num.
overlap.dat contains the overlap of each atom and sum.dat contains the
average values for the whole system.
Usage:
plotpdb -i infile -pdb pdbfile [-het] [-o offset]
Option Type Value Description
------------------------------------------------------------
-i Input Res data file |resnumber value| no header
-pdb Input pdbfile
-het Opt Incudes reading HETATM records with flag
-o Input,Opt 0 Value of the offset if needed
C O V A R
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the covarience matrix from a trajectory and
outputs an eigenfacs type file of the eigenvalues and eigenvectors which
can be further analysed using the rest of this toolbox. The input
trajectories that can be used are:
.prmtop parameter file and .mdcrd trajectory files from amber
.gro parameter file and gmx_dump written trajectory file from gromacs
.CONFIG parameter file and .HISTORY trajectory file from dl_poly
Output files:
average.pdb - average coordinates of the trajectory
rmsd.dat - the rmsd displacement of the atoms from the average
matrix.sdijf - the covarience matrix, only with -mat option
fiteigen.dat - the trajectory coordinates dot product with the
eigenvectors
Usage:
covar -form filetype -p parameterfile -i trajectoryfile
[-ca] [-res] [-s startframe] [-e endframe]
[-skip n] [-mat] [-chain chain.dat]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-res Opt Takes the mass of the residue for the Ca
mass in the analysis, only works with -ca
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-mat Opt Output the covar matrix, matrix.sdijf
-chain Input,Opt File to list the atoms in each custom user
chain
-sv Input,Opt 1 First eigenvector included in plot
-ev Input,Opt 3 Last eigenvector included in plot
F U L L 2 C A
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program converts any imput files to the versions with only the
alpha Carbon atoms included.
Usage:
genENM -pdb pdbfile [-c cut-off] [-f force] [-ccust cfile]
[-fcust ffile] [-mass] [-ca] [-res] [-het] [-hin h]
[-an p]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt Convert the eigenfacs style file
-bfac Input,Opt Convert the mode.bfactors file
-het Opt Includes reading HETATM records
D O M A I N S
VERSION 1.0
Written by:
This program rewrites a pdbfile in order of the domains listed in
input.domain for use with rtb domains.
This program also rewrites the domain eigenfacs file back into the
pdb order.
Usage:
domains -pdb pdbfile [-i matrix]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file
-pdb2 Input,Opt domains.pdb Domain ordered pdb file
-i Input,Opt matrix.eigenfacs Domain ordered eigenfacs file
-het Opt Include reading HETATM records
-rev Opt Sort eigenfacs file instead of pdb
input.domain format:
WRITE('input.domain','(I4,1X,A1,1X,I4,1X,I4)') domb, cdom, doms, dome
atomname is in pdb format
e.g.
| 1 A 10 15
| 2 B 20 30
P R O J E C T
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program projects the eigenvectors onto the pdb file
Usage:
genENM -pdb pdbfile [-i eigenfacsfile] [-s start]
[-e end] [-scale n] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt matrix.eigenfacs eigenvectors file
-s Input,Opt 7 first eigenvector included
-e Input,Opt 31 last eigenvector included
-scale Input,Opt 1 scale factor
-het Opt include HETATMs
E G N P R O J
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program performs a projection on the eigenspace defined by
precalculated eigenvectors and outputs a plotable file over the number of
specified trajectories.
The input trajectories that can be used are:
.prmtop parameter file and .mdcrd trajectory files from amber
.gro parameter file and gmx_dump written trajectory file from gromacs
.CONFIG parameter file and .HISTORY trajectory file from dl_poly
Usage:
eigen_proj -form filetype -p parameterfile -i trajectoryfile
-pdb pdbfile -eigen eigenfacs [-ca] [-s startframe]
[-e endframe] [-sv startvector] [-ev endvector]
[-skip n]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-eigen Input Eigenvectors eigenfacs file name
-pdb Input Average pdb structure matching eigenfacs
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-sv Input,Opt 1 First eigenvector included for analysis
-ev Input,Opt 3 Last eigenvector included for analysis
P D B D I F F
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program projects the eigenvectors onto the pdb file
Usage:
genENM -pdb pdbfile [-i eigenfacsfile] [-s start]
[-e end] [-scale n] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt matrix.eigenfacs eigenvectors file
-s Input,Opt 7 first eigenvector included
-e Input,Opt 31 last eigenvector included
-scale Input,Opt 1 scale factor
-het Opt include HETATMs
S P A C I N G
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program produces a file, dist.dat for plotting the spacing between
atoms.
Usage:
spacing -pdb pdbfile [-ca] [-het] [-lig1]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-ca Opt Calculates Ca model only
-lig1 Opt Assigns each residue in the HETATMs one
average point, only works with -het and
-ca flags as well
-het Opt Includes reading HETATM records
M O V E I N G
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the change in the distance between atoms between
the equilibrium value and the value after applying the eigenvectors.
The output file, movement.dat, can be plotted in gnuplot with the
command:
splot "moving.dat" using 1:2:3 notitle
Usage:
movement -pdb pdbfile -i eigenfacs file [-s start]
[-e end]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input Eigenvector file name
-s Input,Opt 7 First eigenvalue included
-e Input,Opt 31 Last eigenvalue included
T R A J P D B
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the covarience matrix from a trajectory and
Usage:
covar -form filetype -p parameterfile -i trajectoryfile
[-ca] [-res] [-s startframe] [-e endframe]
[-skip n]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-res Opt Takes the mass of the residue for the Ca
mass in the analysis, only works with -ca
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-box Input,Opt 3 box type used
-pbc Opt Use pbcs
-sol Opt Include solvent atoms
