VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Feb 28 2006 - 04:12:02 CST

Dear Ivana,

The APBS plugin creates an interface to the APBS program itsself ... In
order to understand what actually are all the parameters that you need
to set in a APBS run via vmd, you should definetely consult the APBS
webpage (http://apbs.sourceforge.net/). My own advice is: if you really
are new to these type of calculations and want to understand them... try
first to set up a APBS calculation without the vmd plugin (use only
APBS)... This will make it easier for you to get the grip of all the
input and output of APBS ... After that you can use the ".dx" file
created by APBS to visualize it in VMD . (you probably noticed that VMD
has a dx plugin reader) ...

Then...for subsequent calculations you may start to use the vmd plugin
(after you become familiar with APBS) ...

As I said this is just my advice ....

If you need more specific help ... there is also an APBS maillist that
you may use .... or you may contact me directly .. and if I can help I
will ..

Best
vlad

ivana adamovic wrote:

> Hello,
>
> I am quite new in using VMD, so I hope that this question was not
> answered already, if so, please just point me to where the solution of
> the problem was already described.
>
> I would appreciate help on how to obtain electrostatic potential map
> using VMD. Can it run PB calculations or we need to read in files form
> some of the MD codes?
>
> What is done in APBS Electrostatic part of the Analysis section and in
> PME ?
> Could you explain me a set up for both of these parts?
>
> Thanks a lot,
>
> Ivana Adamovic
> 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/