Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS

From: Leonardo Sepulveda Durán (
Date: Fri Jun 24 2005 - 10:33:40 CDT

I dont have information of books, but in there are two tutorial
might be of your interest: "Parameterizing a Novel Residue" and
"Topology File Tutorial". From what i read there you will have to
create parameters for dihedrals , angle and bond stretching terms (and
charges also) for C-S-H triad. But i think there would
problems...because you are changuing a sulfur joined to an aromathic
ring, so maybe the entire ring parameters should be changed (posibly
the partial charge of orto and para carbons may change more, due to
resonant structures). That would be a problem. But read the
par_all22_prot.inp and top_all22_prot.inp, maybe there is parameters
for sulfur joined to an aromatic group, and carbons in that condition.
I guess other place you would visit for information is
forums. I think "Alex" is an expert in the issue. Well, that is all
what i know about it, I never have done QM calculations, but in the
tutorials it seems to be easy.


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