Re: implicit solvent energy calculation

From: Neema Salimi (
Date: Tue Feb 26 2008 - 15:10:25 CST

check out this program

On Feb 26, 2008, at 2:03 AM, wrote:

> Hello,
> I have a trajectory from NAMD in dcd format of a solvated protein,
> and I would like to calculate the energy of ONLY the dry protein.
> With Sander, this can be done doing a implicit solvent energy
> calculation of all the trajectory, but sander cannot read a
> trajectory in .dcd format.
> As far as I know NAMD does not read a whole trajectory, and besides
> it does not permit implicit solvent calculations. Does anyone knows
> an alternative to do this? If the solution is converting the dcd
> trajectory to a crd can this be done?
> Thank you very much for your help, in advance.
> Rebeca García Fandiño Ph. D.
> Parc Cientific de Barcelona
> Barcelona Spain

Neema Salimi

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
Lab Phone: (415) 476-5143

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