[AMBER] many initial systems for a two molecules system

From: Fabian Glaser <fglaser.technion.ac.il>
Date: Wed, 3 Sep 2014 14:26:10 +0300


I would be grateful to get ideas or a sample script that does the following: I would like to create many initial systems as possible for two small molecules which are supposed to interact, including two small molecules, in the following manner:
To start with the two molecules far away from each other (let's say 50 Angs). Start pulling them to each other slowly (let's say 1 Angstrom in each 100 ps) until the final distance is 10 or 15 Angstroms. Once this distance is reached, to pull them apart to 50 Angstroms again, and continue doing this 50 times. In this way I would like to get 50 initial structures where the two molecules are in close contact. Then, I will perform 50 independent MD with these initial conformations.

The problem is I never did something so complex with amber, I would appreciate any sample script or a pointer to sample scripts.

Thanks a lot in advance,


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

Tel: +972 4 8293701
Fax: +972 4 8225153

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Received on Wed Sep 03 2014 - 04:30:02 PDT
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