[gmx-users] error in ffgmxbon.itp
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Jan 8 13:13:23 CET 2011
On 8/01/2011 8:44 PM, delara aghaie wrote:
>
> 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* (-:
>
That's prehistoric. I hope you have a sufficient reason to need to use a
version of GROMACS that predates your water model...
>
> 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.orgfor 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
> *
>
What's going on here?
> 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
>
Somewhere there should be a #define DC_MNC1 <blahblahblah> that's
probably not being found. Where is it?
Mark
> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110108/f1047b26/attachment.html>
More information about the gromacs.org_gmx-users
mailing list