AMBER Archive (2005)

Subject: Re: AMBER: calculating electrostatic potential

From: david.evans_at_ulsop.ac.uk
Date: Tue Jan 25 2005 - 05:24:52 CST

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

--
David Evans
School of Pharmacy
University of London

---- Message from Vlad Cojocaru <Vlad.Cojocaru_at_mpi-bpc.mpg.de> 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
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
>
>-- 
>Vlad Cojocaru 
>Max Planck Institute for Biophysical Chemistry 
>Department: 060 
>Am Fassberg 11, 37077 Goettingen, Germany 
>tel: ++49-551-201.1327 
>e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>home tel: ++49-551-9963204  
>
>
>
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