GROMACS version: 5.1.2
GROMACS modification: No
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I want to do protein-peptide simulation. I am following the steps same as whole protein simulation. However, during topology setup, the amino acids did not get recognized by the system. I am using gromos54a7 as force field.
The peptide is composed of: BEZ NLE KR OAR
BEZ- Benzoic acid
NLE- Norleucine (isomer of leucine)
KR- lysine, arginine
OAR - amino acid domain
I get few warnings from the system:
Starting residue BEZ1 in chain not identified as Protein/RNA/DNA
Starting residue NLE2 in chain not identified as Protein/RNA/DNA
Starting residue OAR5 in chain not identified as Protein/RNA/DNA
Residue ‘BEZ’ not found in residue topology database
Residue ‘NLE’ not found in residue topology database
How I can solve these problems? I want to keep BEZ (even though it is not amino acid residue) in the peptide structure as it plays a role in structural conformational.
Your helps are greatly appreciated. Thank you.