AMBER Archive (2005)

Subject: Re: AMBER: calculating electrostatic potential

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 25 2005 - 12:26:32 CST

Hey Vlad,

I do not know any free software for the thing you want to do. I have done
such mappings using GRASP from Honig Lab. I heard that DelPhi can do the
same thing too, but GRASP is pretty easy to use.

Best,

On Tue, 25 Jan 2005, Vlad Cojocaru wrote:

> 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
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------

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