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

[Mark Abraham]

Yeah, don't use wysiwyg word processors for editing plain text files (else
you will get such smartness tripping you up). Use an editor aimed at them.

Mark

On Tue, 26 Apr 2016 13:59 gozde ergin <gozdeeergin at gmail.com> wrote:

> 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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