AMBER Archive (2008)

Subject: AMBER: Simulating protein conformational changes?

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Fri Aug 01 2008 - 17:42:07 CDT

Hi,
this is more of a methodology question, rather than a specific technical
issue..

We are trying to use Amber to predict whether a particular mutated
protein undergoes conformational changes that are different from the
wild type. Could you suggest a reasonable way to proceed using the tools
that come with Amber?

Thanks in advance for any suggestions

Sasha

David A. Case wrote:
> On Wed, Jun 11, 2008, Khaled Barakat wrote:
>
>> I am trying to use Antechamber to create a prepin file for a zinc ion
>> coordinated with 3 cysteine residues and 1 histedine.
>>
>
> Antechamber doesn't know about metals: you need to prepare files for those by
> hand. Look for papers on simulations of zinc enzymes: some will provide
> details of the force fields they used.
>
> ...dac
>
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