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 > > > >--------------------------------------------------------------------- -- >The AMBER Mail Reflector >To post, send mail to amber_at_scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu > > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu