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

[gozde ergin]

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The problem is quote.

On 26 Apr 2016, at 13:35, gozde ergin <gozdeeergin at gmail.com> wrote:
> 
> I checked it and there is no #include statement in cis-pinonic.itp file.
>> On 26 Apr 2016, at 13:24, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>> 
>> 
>> 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
>> 
>> ==================================================
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>