[gmx-users] grompp - Group protein not found
Peter C. Lai
pcl at uab.edu
Wed Mar 7 21:59:22 CET 2012
Ahh, case sensitivity?
Protein vs. protein?
On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote:
> On 8/03/2012 4:31 AM, Peter C. Lai wrote:
> > Check the molecules section at the bottom of your top file. Each molecule
> > entry there should match the corresponding name given to it in the molecule's
> > own topology (the name under [moleculetype]).
> Those names can match and this error arise because this error is
> probably because the .mdp file refers to "protein" and there is no such
> group generated for the default index groups (used when no -n file is
> * make an index file with such a group and name it "protein,"
> * copy $GMXLIB/residuetypes.dat to your working directory and add your
> protein residues to allow the default generated groups to understand
> your knowledge about what is a protein,
> * name your [moleculetype] the same as your references to it in your
> .mdp file and [molecules] section.
> > On 2012-03-07 05:13:11PM +0000, Lara Bunte wrote:
> >> Hi
> >> I create a file pr.mdp for equilibrating the water around my molecule and used after that the command
> >> grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
> >> And I got tthe error:
> >> Fatal error:
> >> Group protein not found in index file.
> >> Group names must match either [moleculetype] names
> >> or custom index group names,in which case you
> >> must supply an index file to the '-n' option of grompp.
> >> Could you explain that error to me please? How to fix it?
> >> Greetings
> >> Lara
> >> --
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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