VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Feb 27 2009 - 06:49:43 CST

Hi Jianping,

On Thu, Feb 26, 2009 at 7:12 PM, Jianping Lin <jianpingl_at_gmail.com> wrote:
> Hi All,
>
> Anyone by chance has a plugin in VMD that can run MM/PBSA calculations?

A MM/PBSA utility/script has not been yet implemented in VMD. However,
you can always perform MM/PBSA calculations in a semi-automatic way.
For example, you can use the 'Energy' plugin and APBS to calculate the
MM and PB parts. You can also calculate the accessible surface area
using a simple tcl script. Finally, you can estimate the entropy using
the quasi-harmonic approximation (using carma, for example.
http://utopia.duth.gr/~glykos/Carma.html).

Cheers,
Michel

>
> Thanks.
>
> Jianping
>