AMBER Archive (2009)

Subject: [AMBER] Atom Type List

From: Javier Klett (
Date: Mon Jun 22 2009 - 04:54:43 CDT


    I need to classify the atom types of a set of pdb files into the
amber atom type list. For that i used tleab obtaining the "top" and
"crd" files, and afterwards I used "ambpdb" to reconvert them into pdb
files with the "supposedly" amber atom types.

    The problem is that when checking the obtained atom types, i get
atom names that are not in the file "param99.dat" neither in any of the
files ".dat" provided in the "amber10.ffparms.tar.bz2" that I downloaded
in the amber web page. Some of this atom names are:
OE, OG, HH, HD, HB, HG, CG, etc.

    Can any body give me advise of how to do this?

    Thanks very much in advance!

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