Mixing all_36_cgenff with all_36_prot

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Mar 26 2016 - 13:02:27 CDT


My aim, following a chemical modification of a protein, is to assigning
charmm parameters for a bond non-ppeptidic between two amino acids in the
same subunit of the protein. Such a bond does not exist in all_36_prot.

In order to build a suitable patch for psfgen, in a first trial, before
carrying out QM computations, I considered the smallest model that includes
the atoms types for the atoms involved in the new chemical bond, building a
stream file (.rtf and .prm) by using atom types from all_36_cgenff.

My question is, for the couple of residues involved in the chemical
bonding, can I safely build two new residues that result from a mixture of
all_36_cgenff atom types (for the minimum number of atoms to describe bond,
angles dih IC) with the original all_36_prot atom types for the other atoms
in the two residues? That is, something like in the DISU patch.

thanks for advice

francesco pietra

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