Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16
Cl ions using genion and now want to use grompp and then start the simulation
to see the effect of ions on the pressure-area isotherm of the system.
running grompp in gromacs 3.3 I see he following error:
please help em to solve it.let me knoe please what is cpp?
Thanks in advance
D. Aghaie
-bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n indexsalt-Mg.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 dppc-salt-Mg-0.1.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 indexsalt-Mg.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.1#
checking input for internal consistency...
calling cpp...
topoldppc.top:7:20: error: ions.itp: No such file or directory
cpp exit code: 256
Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top >
gromppzVWhWp'
The 'cpp' command is defined in the .mdp file
processing topology...
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours for DPP 64
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 4152
turning all bonds into constraints...
Cleaning up temporary file gromppzVWhWp
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3
Source code file: toppush.c, line: 1264
Fatal error:
No such moleculetype Mg
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
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