[AMBER] how to use cpptraj for pdb files generated from external software

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Wed, 18 Mar 2015 12:34:29 -0400

 Dear Amber users,

I have some hundreds of pdb files generated from external software (like
online server), these pdb files differ from pdb generated by AMBER in term
of naming of hydrogen atom. Is there a way to generate topology file for
these files so that I could use ambertool like cppraj command to calculate
atomic distances, angles etc to compare with corresponding AMBER results ?
For a single pdb, I use leap to get topology file but do not know for a
large no of pdb files.

Thank you for help,
Mahendra Thapa
University of Cincinnati
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Received on Wed Mar 18 2015 - 10:00:02 PDT
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