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/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jan 25 2005 - 18:53:01 PST
