AMBER Archive (2007)

Subject: AMBER: Problem using Ptraj

From: alfredoq_at_fcq.unc.edu.ar
Date: Mon Apr 23 2007 - 10:41:56 CDT

Dear Amber users:
                 I am having troubles to prepare the snapshots for mm_pbsa
analysis. I have the trajectory file and the corresponding prmtop file, wich I
can visualize in VMD without problems. The point is that after striping the
waters and ions with ptraj, and obtaining the new desolvated and deionized
prmtop files, when I try to check the new trajectory, I find that the ligand
atoms are all missplaced, with corrupted binding distances, angles and lenghts.
Obviously, the snapshots for mm_pbsa are also corrupted. I have checked several
times the integrity of the ligand prepin and frcmod file, but everything seems
to be ok. Does anyones have experienced this kind of problems before,
Thank you in advance for the help

Best Wishes

Alfredo Quevedo

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Facultad de Ciencias QuĂmicas - Universidad Nacional de CĂrdoba

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