Dear Justin I want to run a simulation on a system containing DPPC and water(TIP4P-2005). I have in my .top file some included .itp files. they are: lipid.itp dppc.itp tip4p-2005.itp ffgmx-local.itp (this is the name which we have selected for the modified version of ffgmx.itp) in which they are two included files: ffgmxbon-local.itp & ffgmxnb-local.itp I have simulated this system at 310 K without error before. Now I only changed the temp to 270 K in the run.mdp file, now using the grompp command I get this error:(I sent you the command line and the error, below) I do not now what is ffdum.itp (you can see error line below) you can see below also the part of ffgmx-local.itp which the error is about that part. please let me know how to fix the error. thanks for your time --------------------------------------------------------------------
-bash-3.2$ grompp_mpi -c confout-310-500.gro -f run.mdp -n index.ndx -p topoldppc.top -o topol.tpr -np 8 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, 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. :-) grompp_mpi (-: Option Filename Type Description ------------------------------------------------------------ -f run.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c confout-310-500.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topoldppc.top Input Topology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 8 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling cpp... In file included from ffgmx-local.itp:9, from topoldppc.top:3: ffgmxbon-local.itp:125:22: error: ff_dum.itp: No such file or directory cpp exit code: 256 Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top > gromppAjujan' The 'cpp' command is defined in the .mdp file processing topology... ERROR 1 [file "ffgmxbon-local.itp", line 129]: Not enough parameters ERROR 2 [file "ffgmxbon-local.itp", line 130]: Not enough parameters ERROR 3 [file "ffgmxbon-local.itp", line 131]: Not enough parameters ERROR 4 [file "ffgmxbon-local.itp", line 132]: Not enough parameters ERROR 5 [file "ffgmxbon-local.itp", line 133]: Not enough parameters ERROR 6 [file "ffgmxbon-local.itp", line 134]: Not enough parameters ERROR 7 [file "ffgmxbon-local.itp", line 136]: Not enough parameters ERROR 8 [file "ffgmxbon-local.itp", line 137]: Not enough parameters ERROR 9 [file "ffgmxbon-local.itp", line 138]: Not enough parameters ERROR 10 [file "ffgmxbon-local.itp", line 139]: Not enough parameters Cleaning up temporary file gromppAjujan ------------------------------------------------------- Program grompp_mpi, VERSION 3.3 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated ------------------------------------------------------- Thanx for Using GROMACS - Have a Nice Day .................................................................... ------------------------------------------------------------------- [ constrainttypes ] ; now the constraints for the rigid NH3 groups MNH3 C 2 DC_MNC1 line :129 MNH3 CB 2 DC_MNC1 MNH3 CHE 2 DC_MNC1 MNH3 CH1 2 DC_MNC2 MNH3 CH2 2 DC_MNC2 MNH3 MNH3 2 DC_MNMN ; and the angle-constraints for OH and SH groups in proteins: CH2 HS 2 DC_CS line 136 CH2 HO 2 DC_CO CH1 HO 2 DC_CO CB HO 2 DC_CO C HO 2 DC_CO P HO 2 DC_PO
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