Re: AMBER: calculating electrostatic potential

From: <>
Date: Tue, 25 Jan 2005 11:24:52 +0000

You could try APBS, by Nathan Baker. It has a VMD plugin for

David Evans
School of Pharmacy
University of London
---- Message from Vlad Cojocaru <> at
2005-01-25 11:59:48 ------
>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
>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
>visualization . I was using the deep viewer (SPDBV) for proteins but
>doesnt work for nucleic acids.
>  Do you know any freeware (for linux) which can take the amber
>charges, solve the non-linear Poisson Boltzmann equation and then
>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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