Unknown cmap torsion between atoms near modified residue – User discussions

GROMACS version: 5.1.4 2020
GROMACS modification: Yes/No

I’m simulating a single protein with phosphorylated serine-modified amino acid. I’m using charm36-mar2019 ff.
Earlier while converting pdb2gmx the input file showed fatal error many times:
“Residue 34 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.”
But in my input file at residue 34 there is “THR” not GLY.
After many attempts, .gro file was generated without error.
Then, from grompp I obtain the following fatal error:
“Unknown cmap torsion between atoms 440 442 444 447 450” (C N CA C N)
Among these, atom no 450 (i.e. N) is from the modified residue and the other 4 atoms are at the N terminal residue of the modified one.
I looked into a similar previous question by [fchiappori] and checked the cmap.itp file. But, in this file it does not include “C N CA C N”. Also, I am unable to figure out where the problem is and how to tackle it.

I am new to charmm ff and gromacs simulations, please suggest to me what can be done.

Thank you
Shashank

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