RE: implicit solvent energy calculation

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Feb 26 2008 - 13:51:26 CST

Rebeca,

   With VMD, you could cut out the protein selection and write the trajectory to a new DCD file, together with a PDB format file from one of the frames. Then, you can re-build the protein-only PSF file in CHARMM from the PDB file. Use CHARMM to read in the protein-only DCD file and PSF file, and calculate implicitly solvated energies of the frames.
   You could also loop over the DCD file in VMD, select the protein, and write out a PDB file per frame; then, I imagine AMBER could handle the job. There is probably a more efficient way, but I don't use AMBER myself, so I can't say.

Cheers,

Chris
 

> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of regafan_at_usc.es
> Sent: Tuesday, February 26, 2008 3:04 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: implicit solvent energy calculation
>
> 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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