[gmx-users] Group protein not found in indexfile

[Justin Lemkul]

On 11/4/13 1:29 PM, Steve Seibold wrote:
> Hello
> I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files:::: pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp.
>
> When I use grompp  however, I get a fatal error “Group protein not found in index file. Maybe you have non-default groups in  your .mdp file,  while not using ‘-n’ option in grompp”
>
> I’ve looked up this error on-line but I don’t see people getting this error when using multiple chains. I only have protein present and nothing  else. I am obviously doing something incorrect.
>
> I would greatly appreciate any comments that would help me..
>

Please provide:

1. Your exact grompp command
2. Your full .mdp file
3. The gmxcheck output of the .ndx file

-Justin

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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

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