AMBER Archive (2006)

Subject: AMBER:

From: Paweł Gruszczyński (blackrose2_at_wp.pl)
Date: Sat Feb 04 2006 - 03:16:10 CST

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

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