possible bug in trjconv -split. I'm using the following command to export a set of .pdb files from a .xtc trajectory:
trjconv_d -f md_0_1_solv.xtc -o md_0_1_solv_.pdb -s md_0_1_solv.tpr -split 500 After writing the 250th file, gromacs quits with the below error message. By contrast, gromacs completes the full export using -split 5000 instead of -split 500, in which case the total number of files is <250. Cheers, Mike --- Error message: -> frame 62750 time 125500.000 -> frame 62000 time 124000.000 ------------------------------------------------------- Program trjconv_d, VERSION 4.5.5 Source code file: futil.c, line: 905 Fatal error: Library file residuetypes.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Full output: :-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. 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. :-) trjconv_d (double precision) (-: Option Filename Type Description ------------------------------------------------------------ -f md_0_1_solv.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -o md_0_1_solv_.pdb Output Trajectory: xtc trr trj gro g96 pdb -s md_0_1_solv.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 -[no]version bool no Print version 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: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -skip int 1 Only write every nr-th frame -dt time 0 Only write frame when t MOD dt = first time (ps) -[no]round bool no Round measurements to nearest picosecond -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) -clustercenter vector 0 0 0 Optional starting point for pbc cluster option -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, transxy 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 trajectory 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 500 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 If the -sep flag is set, use these many digits for the file numbers and prepend zeros as needed -dropunder real 0 Drop all frames below this value -dropover real 0 Drop all frames above this value -[no]conect bool no Add conect records when writing .pdb files. Useful for visualization of non-standard molecules, e.g. coarse grained ones Will write pdb: Protein data bank file Reading file md_0_1_solv.tpr, VERSION 4.5.5 (double precision) Reading file md_0_1_solv.tpr, VERSION 4.5.5 (double precision) Select group for output Group 0 ( System) has 6517 elements Group 1 ( Water) has 6477 elements Group 2 ( SOL) has 6477 elements Group 3 ( non-Water) has 40 elements Group 4 ( Ion) has 40 elements Group 5 ( CL) has 40 elements Group 6 ( Water_and_ions) has 6517 elements Select a group: 6 Selected 6: 'Water_and_ions' Reading frame 0 time 0.000 Precision of md_0_1_solv.xtc is 0.001 (nm) -> frame 62750 time 125500.000 -> frame 62000 time 124000.000 ------------------------------------------------------- Program trjconv_d, VERSION 4.5.5 Source code file: futil.c, line: 905 Fatal error: Library file residuetypes.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Thanx for Using GROMACS - Have a Nice Day -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
