[AMBER] "closest" command in cpptraj

From: Alfredo Quevedo <alfredoq.fcq.unc.edu.ar>
Date: Mon, 16 Apr 2012 16:57:11 -0300

Hello everyone. I am trying to process a solvated trajectory with
cpptraj with the aim of obtaining the desolvated trajectory including
the 10 water molecules that are close to the ligand (LIG).
In this way I am running the following commands:

trajin Solvated-trajectory.mdcrd
closest 10 :LIG first closestoy archive.dat outprefix closest
trajout Desolvated-trajectory.mdcrd trajectory

What I am getting as result is a trajectory containing only the ligand
(LIG) with the corresponding 10 WAT molecules. How I am supossed to
indicate cpptraj to conserve the rest of the receptor and calculate WAT
distances just based in LIG residue? Why is the rest of the trajectory
striped out?
Thannk you very much in advance for the help,
best regards

Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
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Received on Mon Apr 16 2012 - 13:00:03 PDT
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