GROMACS version:
GROMACS modification: Yes/No
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I am getting an error “Atom O in residue KYT 14 was not found in rtp entry KYT with 31 atoms
while sorting atoms.”
The KYT residue is a custom residue. This is the last residue which connects to sidechain of one of the initial residue through
ester bond by using C-terminal. The KYT residue is parameterized to include the sidechain of the intital residue which connects to the C-terminal.
In order to include the Custom residues and the the ester bond connection the aminoacids.rtp file and aminoacids.hdb has been modified to include them.
Yet I am receiving this error. I presume by this error the pdb2gmx is trying to look for C-terminal O which of course would not be present.
I am using charmm36m forcefield to model the molecule. It is similar to surfactin.
Can you please guide as to how to approach the issue. The peptide has a cyclic part in it.