VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Tue Feb 28 2006 - 09:48:47 CST

Dear Vlad,

Thanks a lot for your answer.

I'll check it out and let you know how it is going.

Ivana

On 2/28/06, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> 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/
>
>
>