[AMBER] Atom reordering for TI

From: Thomas Exner <thomas.exner.uni-konstanz.de>
Date: Tue, 15 Jan 2013 13:25:01 +0100

Dear AMBER users and developers:

I would like to run TI calculations on a set of slightly modified
ligands. The parameters are generated by antechamber (partial charges
are calculated with Gaussian) and I renamed common atom to match in
each ligand. But unfortunately, antechamber generates different atom
orderings in each parameter file and, thus, they are also in different
order in the amber input files. Is there a way to reorder the atoms that
they are consistently ordered in all input files as required for sander.
To be consistent with earlier simulations I still use AMBER10 for the
calculations.

Thank you very much.
Thomas

-- 
________________________________________________________________________________
Dr. Thomas E. Exner
Theoretische Pharmazeutische Chemie & Biophysik
Lehrstuhl Pharmazeutische Chemie
Pharmazeutisches Institut
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 8 (Haus B)
72076 Tübingen
Germany
Tel.:    +49-(0)7071-2976969
Mobil:   +49-(0)171-3807485
Fax:     +49-(0)7071-295637
E-Mail:  Thomas.Exner[at]uni-tuebingen.de
Fachbereich Chemie  und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Germany
Tel.:   +49-(0)7531-882015
Fax:    +49-(0)7531-883587
E-Mail: Thomas.Exner[at]uni-konstanz.de
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Received on Tue Jan 15 2013 - 04:30:05 PST