On 8/2/13 5:57 AM, chinnu657 wrote:
oh, sorry.
So the error is:
Fatal error:
Topology include file "posre.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
There are probably #include statements in the .itp files for the proteins, since
they were originally .top files written by pdb2gmx. You'll need to get rid of
those or otherwise suitably rename them (and then delete the redundant #include
statements in the .top).
-Justin
The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
My topol.top:
;GROMACS toplogy
;
;Include the force field
#include "oplsaa.ff/forcefield.itp"
; Include chain topologies
#include "topol_1AKI.itp"
#ifdef POSRES
#include "posre_1AKI.itp"
#endif
#include "topol_2CDS.itp"
#ifdef POSRES
#include "posre_2CDS.itp"
#endif
;Include water topology
#include "spce.itp"
;Include generic ion topology
#include "ions.itp"
[ system ]
Two proteins in water
[ molecules ] #mols
Protein_1AKI 1
Protein_2CDS 1
SOL 27020
CL- 16
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--
==================================================
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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