VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 25 2011 - 19:51:55 CDT

2011/5/25 Marek Maly <marek.maly_at_ujep.cz>:
> Hello all,
>
> with "APBS Electrostatics" VMD plugin is possible to calculate electrostatic
> potential around given molecule. Molecular surface might be colored
> according
> to potential values but is there any possibility for calculation of mean
> value of
> electrostatic potential on molecular surface (so simply the potential
> average over all grid points
> which represent molecular surface ) in VMD ?

no.

>
> If not, is there any other SW which could do this job if one provide
> molecular structure
> (e.g. *.pdb file) and potential values (i.e. *.dx file) calculated
> previously using "APBS Electrostatics" VMD plugin ?

none that i know if. it is a pretty ill-defined property,
since "molecular surface" is rather arbitrary.
if anything, the integral over a volume is probably more
meaningful, as it would hopefully converge to something
with decreasing density isosurface cutoff.

but then again, you have to be careful to normalize this
correctly, especially for charged molecules.

cheers,
    axel.

> Thanks a lot in advance for any useful comments !
>
>  Best wishes,
>
>     Marek
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.