Keeping water out of the binding pocket with ColVar

From: Wang Yi (dexterwy_at_gmail.com)
Date: Fri Jul 20 2012 - 20:14:41 CDT

• Next message: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Previous message: Cristhian Boetsch: "crossterm error"
• Next in thread: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Reply: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi NAMD experts,

I'm wondering if there's any way to keep the solvent out of the binding pocket of a receptor, to sort of create an empty cavity in a solvent box. I was thinking about using the "lower wall" feature, but not quite sure how to implement it. Or maybe there's better way to do it? Thanks.

Best,
___________________________

Yi (Yves) Wang
Duke University

• Next message: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Previous message: Cristhian Boetsch: "crossterm error"
• Next in thread: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Reply: Aron Broom: "Re: Keeping water out of the binding pocket with ColVar"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:49 CST