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

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================