VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 03 2012 - 13:47:17 CDT

Hi,
  I don't know anything about the eF electrostatics server other than
what I briefly read there after searching in google. From what I read
however, it seems to me that you could do the electrostatics calculation
directly in VMD itself, either through the VMD ABPS plugin, or by using
the VMD volmap plugin, calculating the Coulomb potential map using the
multilevel summation. If your structure has no water or ions, then you
will likely be better off using APBS. If you have a simulation-ready
explicit solvent model, then you can use the VMD volmap tool. Other than
those two suggestions, I don't have other ideas for how to get that eF-surf
file to load into VMD at this moment.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 03, 2012 at 06:33:21PM +0200, Oliver Schmetzer wrote:
> Dear All,
>
> I use VMD since many years, however I now got an electrostatic potential
> calculation which i want to open in VMD. My bioinformatics course is long
> ago, so I need some help. The file I have is a efvet XML file or also a
> molscript file and I want to convert one of it to PDB. It was done form
> the eF-surf server at PDB-japan as all other servers crashed on my model.
> Is there any idea how to convert it?
>
> I can open it in JV viewer, however there are so many bugs in this program
> that I cant do anything.
>
> Btw: maybe anyone has experiences with peptide to protein docking (I have
> several peptides which I want to dock and it will take long, the only idea
> I have is to use direct charge interaction as constrained as the charge is
> extreme)
>
>
>
> Many thanks,
>
> Oliver
>
>
>
>
>
>
>
> Dr. Oliver Schmetzer
>
> Max-Delbru:ck-Centrum for molecular medicine
>
> Molecular Immunotherapy
>
> Robert-Roessle-Str. 10
>
> 13125 Berlin
>
> Germany
>
>
>
> Charite University Medicine Berlin
>
> Clinic for Hematology and Oncology
>
> Augustenburger Platz 1
>
> 13353 Berlin
>
> Germany
>
>
>
> private address:
>
> Jaegerstr. 70
>
> 10117 Berlin
>
> Germany
>
>
>
> ----------------------------------------
>
> clinic: +49 30 8445 2338 (CBF)
>
> mobile: +49 171 783 8355 lab:
> +49 30 9406 2830
>
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> 9406 2695
>
> private fax: +49 30 7407 8038 lab Fax: +49
> 30 9406 2698
>
> e-mail: oliver.schmetzer_at_gmx.net
> oliver.schmetzer_at_charite.de
>
> ----------------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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