From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Mar 28 2016 - 14:36:33 CDT
I recently did something along these lines to build a sulfotyrosine patch from the combination of a CGENFF-paramaterised model compound and the existing all_36 tyrosine residue. Worked fine for me.
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> On 27 Mar 2016, at 5:15 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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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