[gmx-users] Topology include file " " not found

gozde ergin gozdeeergin at gmail.com
Tue Apr 26 11:57:13 CEST 2016

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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "charmm27.ff/ions.itp"

 [ system ]
; title from mol2 input

 [ 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.

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