Hi everyone!
I added a residue on the gromacs 4.5.3 I have. I followed the instructions as
indicated in the "Adding A Residue to a Force Field" with this link
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue.
I added the residue to residuetypes.dat and indicated it as a carbohydrate.
The topology in fact was able to write it down as a carbohydrate.
Generating a topology went well with pdb2gmx, editconf, genbox, energy
minimization. However, I encountered the following error when I was about to do
an NVT equilibration.
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Program grompp, VERSION 4.5.3
Source code file: readir.c, line: 1316
Fatal error:
Group protein not found in indexfile.
Maybe you have non-default groups in your mdp file, while not using the '-n'
option of grompp.
In that case use the '-n'option.
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In response, I created an index file using make_ndx. The index file was able to
generate correctly the molecule indices and identified it correctly as
indicated in the residuetypes.dat and carbohydrate.rtp
And then I tried (again) the following command:
$ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr.
It still generates the same error as above. Please help
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