AMBER: calculating electrostatic potential

From: Vlad Cojocaru <>
Date: Tue, 25 Jan 2005 11:59:48 +0100

Dear Amber community,

   I am trying to calculate the electrostatic potential of some RNA
molecules and map it on a molecular surface. I dont have Delphi and I
was trying to use MEAD but I ran into problems such as I couldnt
automatically create the fpt file and I couldnt find any software for
visualization . I was using the deep viewer (SPDBV) for proteins but it
doesnt work for nucleic acids.

  Do you know any freeware (for linux) which can take the amber partial
charges, solve the non-linear Poisson Boltzmann equation and then maybe
another program for visualization.
  I am working on a Suse Linux 9.0 workstation.

Thank you

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Tue Jan 25 2005 - 11:53:01 PST
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