On 8/23/13 3:29 AM, afsaneh maleki wrote:
Dear GMX users,
To generate a topology file for an arbitrary molecule (TP) on graphite
surface, I used g_x2top program to generate “TP.itp” file and I manually
construct "graphite.itp" file.
Generated topology file is as the following:
#include "./oplsaa.ff/forcefield.itp"
#include "TP.itp"
#include "graphite.itp"
[ system ]
TP ON GRAPHITE
[ molecules ]
;molecule name nr.
TP 2
grap 6400
…….
And the graphite.itp is as the following:
[ moleculetype ]
; name nrexcl
grap 1
[ atoms ]
; nr type resnr residu atom cgnr charge
1 opls_145 1 grap C 1 0.000
I run grompp for EM with this command line: grompp -f *.mdp –c *.gro -p
*.top -o *.tpr
It gave me the following error:
………
Fatal error:
Syntax error - File ffnonbonded.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
…….
I know things in the [ molecules ] section need to line up with what's in
the *.gro file.
True, but not relevant in this case - grompp never gets past the initial stages
of parsing the force field, let alone the system-level information.
Also I looked at that link but I don’t know how to solve this problem.
And other question is:
Do I need to make “nonbonding.itp” to insert in topology file for
introducing nonbonding interaction of graphite with TP molecule?
No, but apparently something is screwed up in the parent force field. Are you
introducing new atom types in either of your molecule .itp files? It seems that
grompp is complaining about the formatting of one of the force field files,
though - have you altered them in any way? Is there any reason you need a local
version of OPLS-AA? Does #including the original OPLS-AA force field instead of
the local one fix the issue?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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