[gmx-users] Protein in energygrp_excl is not an energy group

[Justin Lemkul]

On 4/22/14, 9:12 AM, Rebeca García Fandiño wrote:
> Hi,
> I am trying to use g_membed to insert a protein into a membrane, and for that I am following the instructions indicated in the help-command.
> I am trying to create a .tpr file with the following options included in the .mdp file.
>   - integrator      = md
>   - energygrp       = Protein
>   - freezegrps      = Protein
>   - freezedim       = Y Y Y
>   - energygrp_excl  = Protein Protein
>
> When I try to generate this .tpr file:
>
> grompp -c all_solvated.gro -p topology.top -f prod.mdp -o membed.tpr -n index.ndx, I get this error:
>
>
> Fatal error:
> Protein in energygrp_excl is not an energy group
>
> My protein has 4 chains, but I have a group in index.ndx called Protein, so I don' t know which is the problem. Why is not grompp recognizing energygrp_excl  = Protein Protein???
>

Since "energygrp" is not a keyword ("energygrps" is what you want), then the 
groups are not being defined.  There should be an error from grompp about the 
unrecognized keyword "energygrp," though.  Maybe it doesn't get that far in the 
processing since it bails out when trying to parse through the energygrp_excl.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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