**From:** L. Michel Espinoza-Fonseca (*mef_at_ddt.biochem.umn.edu*)

**Date:** Mon Jun 18 2007 - 14:02:46 CDT

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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>:

*>
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*> Hi all...
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*>
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*> Im performing some MMPBSA calculations and I want to know if it is possible
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*> to perform Normal Mode Analysis to obtain the entropic contribution of the
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*> solute in the MMPBSA ecuation using NAMD. Or should I use another software
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*> such as CHARMM ?? any help please..!!!
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*>
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*> Raśl Araya
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*> Universidad de Chile
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*>
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*> ________________________________
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*> Se uno de los primeros en probar Windows Live Mail. Windows Live Mail.
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