From: Taras Pogorelov (
Date: Wed May 03 2006 - 19:39:09 CDT

Dear Raul,

To recover the "molecular mechanical" energy (Eelec, Evdw, Egeom) you can
certainly use NAMD2 with CHARMM. I would suggest though to have not a
single frame included into the calculations, but have an MD run for
long enough, so that the standard errors on the energy components will be
small. For the references on MM-PBSA, see David Case 2003-2004, Kollman

Hope that this helps.

Have a great day,


Taras Pogorelov
Chemical Physics, University of Illinios, Urbana

 On Wed, 3 May 2006, Raul Araya Secchi wrote:

> Dear NAMD users:
> I want to do some MM-PBSA calculations, for which I run a dynamic on NAMD
> using CHARMM22 parameters. Now I want to do the Emm part of the
> calculation whic involve a molecular mechanic calculation of every
> force-field potential energy vlaues with out cutoff for non-bond
> interactions. But the program I wantet to use for that (DeCipher from
> InsightII) canot do such potential calculation for the CHARMM force
> field. So I want to know wich other program(s) can be usefull for that
> (exept AMBER which I dont have). Can NAMD be used? For rxample by runing
> a one frame dynamic with no cut-off?
> Please Help
> Raul Araya
> CGB_Universidad Catolica de Chile
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