Hi Fabian,
Are the two molecules the same drug? If this is the case, you just need to get parameters for one molecule. Otherwise, you need to perform the same procedure for each one of the two drugs. For instance, you'll get a set of files for each drug and you should be able to call them inside your leap script.
Best,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC
7013, Cincinnati OH 45229
=========================================
El Jueves, 27 de marzo, 2014 9:23:14, Fabian Glaser <fglaser.technion.ac.il> escribió:
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 - 07:00:04 PDT
