Grompp name matching error

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1

GROMACS version:2020
GROMACS modification: Yes/No
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Dear GROMACS users,
I got the following error.

group Protein_chain_A referenced in the .mdp file was not found in the 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.

Group names are the same in the mdp file and the top file [moleculetype]
Should I create an index file in this case? If yes, how to generate an index file that has 13 groups?

Thank you so much

2

Hi,
you can generate an index file using gmx make_ndx tools ( gmx make_ndx — GROMACS 2021.2 documentation) . There is no restriction in the number of group you can generate.
For what you need the group in mdp?
best regards
Alessandra

3

Dear Alessandra,

Thank you so much for your reply.
I want to make the groups in mdp to define the pull groups to do AWH