AMBER Archive (2008)

Subject: Re: AMBER: setbox for solvateoct model

From: David A. Case (
Date: Fri Feb 15 2008 - 20:52:14 CST

On Fri, Feb 15, 2008, Wang, Xuelin wrote:
> I am trying to mutant an amino acid after equilibration of wide-type protein
> in TIP3PBOX water box.
> 1. I made a pdb file from rst and top files of WT protein.

You don't specify whether these files have the waters in them or not.

> 2. I did mutation and reload the new pdb to xleap to generate new top and
> crd file.
> 3. then I run a restrained MD to relax the mutant residue by freezing
> other residues.

same question for the above two steps.

Generally, I think you should take the protein (only) part of the mutated
structure (that you may have refined) and re-solvate it with the solvateOct
command. This will generate the proper box information. Of course, you need
to re-equilibrate, but that is probably inevitable after a mutation.


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