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.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
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 05 2006 - 06:10:07 PST
