[ccp4bb] energy minimise ligand model

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Color of heme containing Xtals
From: Dominique BOURGEOIS dominique {- dot -} bourgeois {- at -} IBS {- dot -} FR
Date: 2008-03-14

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From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-03-14

Subject: energy minimise ligand model
From: Thomas Edwards T {- dot -} A {- dot -} Edwards {- at -} LEEDS {- dot -} AC {- dot -} UK
Date: 2008-03-14

Dear BB,

I have a structure of a protein domain that binds to a peptide ligand containing either a lysine or an arginine. There are homologs in the PDB with the peptide in complex both with lysine and arginine.
I would like to model both alternative ligands bound to the new domain.
It looks like there is a slightly narrowed binding site in my new struture for the end of a lysine side chain, so I'm speculating that the preference will be for lysine over arginine, but I'd like to do something like an energy minimisation and see whether either there is a lower energy complex for the ligand with lysine, or if the arginine moves to an alternate binding site - there is a possible alternate site.
Can anybody suggest a quick and easy (idiots) way of doing this?

Many thanks. Again,

Ed

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Color of heme containing Xtals
From: Dominique BOURGEOIS dominique {- dot -} bourgeois {- at -} IBS {- dot -} FR
Date: 2008-03-14

Next message:
Subject: exclude range within data in scala , discontinuous run in scala problem
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-03-14