[gmx-users] trjconv -f .cpt -s .tpr -o .gro
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Thu Nov 6 04:24:15 CET 2008
Hello,
has anybody successfully used trjconv to obtain a .gro file from a
.cpt file in gromacs 4.0?
Thanks,
Chris.
[cneale at rb17 16core]$ /work/cneale/exe/gromacs-4.0/exec/bin/trjconv -f
test.xtc -s test.tpr -o my.gro
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in Calculating Stuff
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
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.
:-) /work/cneale/exe/gromacs-4.0/exec/bin/trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f test.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-o my.gro Output Trajectory: xtc trr trj gro g96 pdb
-s test.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy, translation
or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trj file after this time (ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 Prepend file number in case you use the -sep flag
with this number of zeroes
-[no]ter bool no Use 'TER' in pdb file as end of frame in stead of
default 'ENDMDL'
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
Will write gro: Coordinate file in Gromos-87 format
Reading file test.tpr, VERSION 4.0 (single precision)
Reading file test.tpr, VERSION 4.0 (single precision)
Select group for output
Opening library file /home/cneale/gromacs/top/aminoacids.dat
Group 0 ( System) has 59152 elements
Group 1 ( Protein) has 5060 elements
Group 2 ( Protein-H) has 2636 elements
Group 3 ( C-alpha) has 314 elements
Group 4 ( Backbone) has 942 elements
Group 5 ( MainChain) has 1258 elements
Group 6 (MainChain+Cb) has 1542 elements
Group 7 ( MainChain+H) has 1556 elements
Group 8 ( SideChain) has 3504 elements
Group 9 ( SideChain-H) has 1378 elements
Group 10 ( Prot-Masses) has 5060 elements
Group 11 ( Non-Protein) has 54092 elements
Group 12 ( POPC) has 13728 elements
Group 13 ( SOL) has 40360 elements
Group 14 ( NA+) has 4 elements
Group 15 ( Other) has 54092 elements
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 1400.000
Precision of test.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Reading frame 7 time 1470.000 -> frame 7 time 1470.000
[cneale at rb17 16core]$ /work/cneale/exe/gromacs-4.0/exec/bin/trjconv -f
test.cpt -s test.tpr -o my.gro
:-) G R O M A C S (-:
S C A M O R G
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
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.
:-) /work/cneale/exe/gromacs-4.0/exec/bin/trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f test.cpt Input Trajectory: xtc trr trj gro g96 pdb cpt
-o my.gro Output Trajectory: xtc trr trj gro g96 pdb
-s test.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy, translation
or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trj file after this time (ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 Prepend file number in case you use the -sep flag
with this number of zeroes
-[no]ter bool no Use 'TER' in pdb file as end of frame in stead of
default 'ENDMDL'
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
Will write gro: Coordinate file in Gromos-87 format
Reading file test.tpr, VERSION 4.0 (single precision)
Reading file test.tpr, VERSION 4.0 (single precision)
Select group for output
Opening library file /home/cneale/gromacs/top/aminoacids.dat
Group 0 ( System) has 59152 elements
Group 1 ( Protein) has 5060 elements
Group 2 ( Protein-H) has 2636 elements
Group 3 ( C-alpha) has 314 elements
Group 4 ( Backbone) has 942 elements
Group 5 ( MainChain) has 1258 elements
Group 6 (MainChain+Cb) has 1542 elements
Group 7 ( MainChain+H) has 1556 elements
Group 8 ( SideChain) has 3504 elements
Group 9 ( SideChain-H) has 1378 elements
Group 10 ( Prot-Masses) has 5060 elements
Group 11 ( Non-Protein) has 54092 elements
Group 12 ( POPC) has 13728 elements
Group 13 ( SOL) has 40360 elements
Group 14 ( NA+) has 4 elements
Group 15 ( Other) has 54092 elements
Select a group: 0
Selected 0: 'System'
Segmentation fault
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