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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Aug 03 2008 - 06:07:56 PDT
