no need to define this, if you load the coordinates it will be handled by
the force field. Cis/tran differences are simply coordinate changes, and
since it is the same amino acid you don't need anything different.
you might want to read some of the recent work by Donald Hamelberg, though,
he has done work on cis/trans isomerization and energy differences.
On Tue, Mar 9, 2010 at 7:31 AM, Francesca Cantini <cantini.cerm.unifi.it>wrote:
>
>
> Dear all,
>
> one of the proline residue in my protein has cis conformation.
> I would like to ask you how and where I have to define a cis-proline when I
> run sander ?
>
> best regards
> thanks
> Francesca Cantini
>
> At 08.14 09/03/2010, you wrote:
>
>> Hi
>>
>> I need to minimize a protein which has ATP bound to it... Can anyone
>> please tell me which force filed to be used for this purpose?Do we need to
>> mention any extra dat file for ATP?
>>
>> --
>> Thanks & Regards
>>
>> Deepti Nayar
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>>
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Received on Tue Mar 09 2010 - 05:00:03 PST
