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
--
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