Re: Dihedral scan in NAMD?

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jun 24 2008 - 02:23:53 CDT

Chris is completely right: I completely forgot about ABF!

My apologies to Milla for the incomplete information and to Chris for
the terrible omission :)

Cheers,
Michel

On Mon, Jun 23, 2008 at 10:21 PM, Chris Chipot
<Christophe.Chipot_at_edam.uhp-nancy.fr> wrote:
> Dear Milla,
>
>
> contrary to what Michel think, a dihedral scan can be achieved in
> NAMD using the adaptive biasing force approach, which yields the
> associated free energy. For details, see:
>
> http://www.edam.uhp-nancy.fr/ABF/
>
> Additional restraints can be enforced while scanning the torsion
> of interest.
>
>
> Chris Chipot
>
>
>
> L. Michel Espinoza-Fonseca a écrit :
>>
>> Dear Milla
>>
>> As far as I know, you cannot do that with NAMD -at least in a
>> straightforward way. Monte Carlo conformational search or a genetic
>> algorithm-type of method would be the most suitable for that, but none
>> of these methods have been yet implemented in NAMD.
>>
>> An alternative (but fuzzy) way to do it would be a set simuleated
>> annealing runs, but I'm not sure if this would be the most suitable
>> method for a correct dihedral search.
>>
>> Cheers,
>> Michel
>>
>> On Mon, Jun 23, 2008 at 5:06 PM, Kamilla Kopec <ozero22_at_yahoo.co.uk>
>> wrote:
>>>
>>> Dear NAMD users,
>>>
>>> Does anyone know a simple way to do a dihedral scan in NAMD? I know how
>>> to
>>> fix and constrain specific atoms. How would I scan round a chosen
>>> dihedral
>>> in e.g. 10 degree increments while keeping others fixed?
>>>
>>> Best Regards
>>>
>>> Milla
>>>
>>>
>>> ________________________________
>>> Sent from Yahoo! Mail.
>>> A Smarter Email.
>>
>>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Equipe de dynamique des assemblages membranaires
> Unité mixte de recherche CNRS/UHP No 7565
> Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
> B.P. 239 Fax: (33) 3-83-68-43-87
> 54506 Vandoeuvre-lès-Nancy Cedex
> E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
> http://www.edam.uhp-nancy.fr
>
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