[gmx-users] Re: topology and coordinate file not matching after grompp

[Justin Lemkul]

On 8/2/13 5:57 AM, chinnu657 wrote:
> oh, sorry.
>
> So the error is:
> Fatal error:
> Topology include file "posre.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>

There are probably #include statements in the .itp files for the proteins, since 
they were originally .top files written by pdb2gmx.  You'll need to get rid of 
those or otherwise suitably rename them (and then delete the redundant #include 
statements in the .top).

-Justin

> The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
>
> My topol.top:
> ;GROMACS toplogy
>
> ;
> ;Include the force field
> #include "oplsaa.ff/forcefield.itp"
>
>
> ; Include chain topologies
>
> #include "topol_1AKI.itp"
> #ifdef POSRES
> #include "posre_1AKI.itp"
> #endif
>
> #include "topol_2CDS.itp"
> #ifdef POSRES
> #include "posre_2CDS.itp"
> #endif
>
> ;Include water topology
> #include "spce.itp"
>
> ;Include generic ion topology
> #include "ions.itp"
>
> [ system ]
> Two proteins in water
>
> [ molecules ]	#mols
> Protein_1AKI	1
> Protein_2CDS	1
> SOL         27020
> CL-               16
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010309.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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