implicit solvent energy calculation

From: regafan_at_usc.es
Date: Tue Feb 26 2008 - 04:03:49 CST

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 done...how can this be done?
Thank you very much for your help, in advance.

Rebeca García Fandiño Ph. D.
Parc Cientific de Barcelona
Barcelona Spain
regafan_at_usc.es

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