Re: Normal mode analysis

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Jun 18 2007 - 14:02:46 CDT

Hi Raul,

In its current form, NAMD does not perform NMA. If you own a CHARMM
license, then I'd suggest you to use it for such purpose.

One more thing: NMA is a very expensive way to calculate the entropy
(you need to perform energy minimization of N conformations taken from
your trajectory, for example), so you also might find useful the
quasi-harmonic approximation using a weight-mass covariance matrix.
I've done MMPBSA using NAMD to calculate the MM energies, APBS to
calculate the solvation contribution and the quasi-harmonic
approximation to calculate the entropic term, and so far it has worked
quite well.

Cheers,
Michel

2007/6/18, Raul Araya Secchi <arayasecchi_at_hotmail.com>:
>
> Hi all...
>
> Im performing some MMPBSA calculations and I want to know if it is possible
> to perform Normal Mode Analysis to obtain the entropic contribution of the
> solute in the MMPBSA ecuation using NAMD. Or should I use another software
> such as CHARMM ?? any help please..!!!
>
> Raśl Araya
> Universidad de Chile
>
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