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.
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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> On 27 Mar 2016, at 5:15 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Hello:
>
> 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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