VMD-L Mailing List

From: Jian Zou (jianzou_at_gmail.com)
Date: Wed Apr 23 2008 - 09:45:58 CDT

how about using "measure contacts" in VMD to find the smallest cutoff
with a non-zero result

gromacs has a command "g_mindist" which can also do this job

or you may write a simple script by yourself

On Wed, Apr 23, 2008 at 10:02 AM, <politr_at_huji.ac.il> wrote:
> Dear All,
> I'm trying to find some command that allows me to find the smallest
> distance between water molecule (let say oxygen) and my protein.
> Regina
>