Dear David:
Thank you very much. Using mol2 files solved the problem.
Best.
Thomas
David A Case wrote:
> On Tue, Jan 15, 2013, Thomas Exner wrote:
>>
>> 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.
>
> Are you using a prepi format in antechamber? If so, don't; use mol2 instead.
> I think(!?!) antechamber will preserve the atom order for formats other than
> prepi. Not sure, though.
>
> ...dac
>
>
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--
________________________________________________________________________________
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 - 08:00:05 PST
