[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro

[Justin Lemkul]

On 3/16/15 7:12 AM, Antara mazumdar wrote:
> Hi,
> I am trying to minimise a coarse grained system having DOPC lipid bilayer,
> a dimeric protein and water. The mdp file has DOPC, Protein and W as
> coupling groups and my topology file also mentions the number of each
> correctly. However while running grompp i am getting *Something is wrong in
> the coordinate formatting of file system.gro* error. No such molecule type
> error does not come now.
>

So now, instead of having a broken topology (or maybe grompp never even gets 
that far), you've altered the coordinate file in some way that the format is 
broken.  Without knowing what you're doing or why you're doing it (usually 
there's no reason to play with the contents of a .gro file manually), there's 
nothing to say here.

-Justin

-- 
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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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