On 4/26/16 5:57 AM, gozde ergin wrote:
Dear all,
I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the
tool.top.
;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"
; Include chain topologies
#include “cis-pinonic.itp"
; Include water topology
#include "charmm27.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "charmm27.ff/ions.itp"
[ system ]
; title from mol2 input
LIG
[ molecules ]
; molecule name nr.
cis-pinonic 64
When I try to minimize the system this is the error that I’m getting,
grompp -f minim.mdp -c lig.gro -p topol.top -o em.tpr
Fatal error:
Topology include file " " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
What is that mean?
I thought maybe there is an invisible line so I did also dos2unix however the
error is still there.
Are there any #include statements within your .itp files (e.g. cis-pinonic.itp)
that might be triggering this?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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