AMBER Archive (2008)

Subject: Re: AMBER: How to build a dimer using amber

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 15 2008 - 11:18:14 CST

On Tue, Jan 15, 2008, Reena ..... wrote:
>
> I am satisfied with the Hex results...Best solution file was saved as a odb
> file which was then used as an input for sander.....My problem is I want to
> study the other geometries also for the dimer formation viz...
> 1) Parallel
> 2) Head to head ( N-terminal....N-terminal)
> 3) Head to tail ( N-terminal---C-terminal)
> 4) Antiparallel etc....

Amber is not a very good platform for model-building of intial structures.
What you describe is possible in xleap, but not very easy or intuitive. Since
these are quite small systems, you might want to consider a quantum chemistry
based program -- others on the list may chime in with their suggestions.

...good luck....dac

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