[gmx-users] grompp error (segmentation fault)in gromacs version 5.0.6

Justin Lemkul jalemkul at vt.edu
Tue Aug 9 13:39:41 CEST 2016

On 8/9/16 2:51 AM, iamdsoumi wrote:
> Hi,
>     I carry on md run on protein-dna complex using  AMBER99SB-ILDN force
> field. Here I state my problem.
>        gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top
> -water tip3p -ignh
>       it compile successfully.
>           gmx_mpi editconf -f em267_processed.gro -o em267_newbox.gro -c -d
> 1.0 -bt cubic
>         it compile successfully.
> gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o em267_solv.gro
> it compile successfully.
> gmx_mpi grompp -f em.mdp -c em267_solv.gro -p topol.top -o em267_ions.tpr
> Here is the problem.
> gromacs states
> Ignoring obsolete mdp entry 'title'
> NOTE 1 [file em.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
> Setting the LD random seed to 1779290498
> WARNING 1 [file topol_DNA_chain_D.itp, line 5]:
>   Too few gb parameters for type localhost.localdomain
> Couldn't find topology match for atomtype localhost.localdomain
> Segmentation fault (core dumped)
> I always take back up of the trajectory file in my external hard disk and
> delete the data from gpu.
> What is the problem ?Problem even exists in  pdb which can be run foremerly
> without any problem.Does anyone know how to solve this issue?

grompp is telling you the problem:

"Couldn't find topology match for atomtype localhost.localdomain"

Since I sincerely doubt that "localhost.localdomain" is a valid atom type, 
likely you've corrupted the topology somehow by inserting some text related to 
the parallel setup of your cluster.



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


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