AMBER Archive (2007)

Subject: Re: AMBER: Ptraj: watershell and distance

From: Pavan G (pavanamber_at_gmail.com)
Date: Tue Jan 30 2007 - 16:01:07 CST

Hi Esther,

If you are trying to calculate the number of water molecules around say
molecule A (which could be a protein), image the coordinates using "image
familiar com :protein" and then use watershell or distance between water and
A. This will ensure that the com of A is fixed.

Hope this helps.

Pavan

On 1/30/07, Esther Brugger <esther_brugger_at_yahoo.com> wrote:
>
> Hi, everyone,
>
> When I use "watershell" command in the Ptraj to calculate the number of
> the waters in a certain distance, I am just thinking, is it possible to
> calculate this number within a centain distrance from the center of mass of
> the molecule?
>
> I have the same problem when I use "distance" command to calculate the
> distance between the specified atoms to the center of mass of the molecule.
>
> Thanks a lot for your any help!
>
>
> Esther B.
>
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