Re: [AMBER] Urea box: artifacts or just a special distribution?

From: David A Case <>
Date: Wed, 20 Jul 2011 12:41:58 -0400

On Wed, Jul 20, 2011, Na Le Dang wrote:

> I have a question regarding the distribution of urea and water molecules
> when a protein is solvated in a 8M urea box using tleap.
> When I check the pdb file in Chimera, there are crossed gaps in the middle
> sections of the protein-urea box

This sounds normal -- tleap does not do a fanstastic job of solvating things.
Our bias is to have the initial volume somewhat too large, and to rely on
constant pressure equilibration to push things together to create the final
starting configurations.


AMBER mailing list
Received on Wed Jul 20 2011 - 10:00:02 PDT
Custom Search