VMD-L Mailing List

From: Alan Wilter Sousa da Silva (alan_at_biof.ufrj.br)
Date: Mon Feb 25 2002 - 12:15:52 CST

Hi VMD-list.

        Amazing, fantastic VMD!

        But I have a problem. Since I don't have Insight/Delphi, I'm
trying to plot elect. pot. molecular surface with what I have.
        (1) First, loading a pdb file with charges (using beta or
occupancy column). Then using MSMS and change colour represantation (RWB)
to beta (or occupancy, whatever I set in the pdb file) results look fine
but I don't think it's right, I mean, (2) I would like to see a surface
composed of discretes points and had accounted every atom charge
interaction (Coulomb, epslon=80) over every point of the grid surface.
Maybe, it's what potsurf script does, but not what (1) does.
        So, I have a Connolly adapeted program to our situation, which
calculates a point-surface (Connolly, probe 1.4) with charges values
attributed as desired in (2) but now I'm looking for a way to show it as
a graphic surface.
        I'm sorry if I couldn't make myself clear, but I want to find a
way to make VMD represents my data source in a surface.
        My point-surface data is built by as many as need points to cover
the molecular Connolly surface with each point having its 3 spatial
coordnates and its charge value (using pdb format I can see a sketch of
what I expect).
        I would thank in advance any attention dedicated to my problem.

Sincerely,

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil