AMBER Archive (2006)

Subject: Re: AMBER:

From: David Mobley (dmobley_at_gmail.com)
Date: Sat Feb 04 2006 - 12:06:23 CST


Maybe there is a way to do this in AMBER itself, but I'd probably do
something like compute all of the ligand-protein distances you're
interested in, then load the data into Matlab or Python and it by
which are closest in each frame.

David

On 2/4/06, Paweł Gruszczyński <blackrose2_at_wp.pl> wrote:
> Dear Amber users!
>
> I would like do count distances between ligand & protein im my
> dynamics file. What I have to do if I want to have in my output file
> closest distances between lingan and protein in each frame?
>
> I have tried to use carnal with this example:
>
> #Simple Coordinate Averaging
> FILES_IN
> PARM p1 wi1.top;
> STREAM s1 md1_wi1.mdrst;
> FILES_OUT
> DISTRIBUTION d1 file MIN;
> DECLARE
> GROUP g1 (RES 1-264);
> GROUP g2 (RES 265);
> OUTPUT
> DISTRIBUTION d1 0.0 5.0 5 DIST g1 g2;
> END
>
>
> but in the output I have only closest distances in the dynamics, and
> I would like to get anwset which RES/ATOMS are closest tho the ATOM
> from my ligand in each frame.
>
> Please help me
> Pawel Gruszczynski
>
> ----------------------------------------------------
> Chuck nie musi dzwonić za darmo, to ludzie dzwonią do niego...
> przez Spika: http://klik.wp.pl/?adr=www.spik.wp.pl&sid=644
>
>
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