[gmx-users] grompp error

Peter C. Lai pcl at uab.edu
Tue Apr 3 21:58:27 CEST 2012

Probably consult the tutorials to determine what T-coupling groups to use.

Generally, Water_and_ions with a separate Protein as 2 T-coupling groups when
dealing with a globular protein in water, but you will have to determine if
that is appropriate for your particular system (i.e. if there are ligands, 
multi-molecule complexes, etc. involved it will probably be different).

On 2012-04-03 11:51:01AM -0700, Eduardo Oliveira wrote:
> Hi all,
> After i ran grompp I've the following message:
> Fatal error:
> 3 atoms are non part of any of the T-coupling groups
> It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp
> genion_d  -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top
> grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr
> Additional information: I'm running GROMACS 4.5.5
> Regards.

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Peter C. Lai			| University of Alabama-Birmingham
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