Thanks a lot,
OK, could you please suggest a good alternative to parametrize two drug like molecules for MD on amber??
Or it is the wrong tool?
Thanks a lot,
Fabian
On Mar 27, 2014, at 3:19 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Mar 27, 2014, Fabian Glaser wrote:
>>
>> I am trying to use antechamber for a drug, which works great for
>> one molecule, but if I use a pdb with two copies of the molecule,
>> antechamber never ends:
>>
>> Total number of electrons: 768; net charge: 0
>>
>> Running: /Users/fabian/TOOLS/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
>
> This is a very large system; beyond that, sqm is trying to find an energy
> minimum. If you have two molecules, the energy minimum might be with the
> molecules arbitarily far apart, and sqm will never complete the job.
>
> Short answer: don't do that. Antechamber is designed to work with single
> molecules.
>
> ....dac
>
>
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_______________________________
Fabian Glaser, PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Thu Mar 27 2014 - 06:30:04 PDT
