[gmx-users] trjconv -f .cpt -s .tpr -o .gro
Berk Hess
gmx3 at hotmail.com
Thu Nov 6 11:08:13 CET 2008
Hi,
This is a bug caused by last minute additions of some stuff to the checkpoint file.
I have fixed it for 4.0.1.
Berk
> Date: Wed, 5 Nov 2008 22:24:15 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] trjconv -f .cpt -s .tpr -o .gro
>
> 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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