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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
