Re: Calculate energy of a residue using NAMD energy

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jan 30 2018 - 20:51:50 CST

Dear Monika,
namdenergy is a proper vmd plugin. Is there any reason that you're trying
to use an old downloaded version rather than using the package that comes
with vmd?
package require namdenergy
should make the text interface available. See
http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/ for how to use it.
Best,
Peter

On Mon, Jan 29, 2018 at 10:22 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Dear all,
>
> I want to calculate the total energy of a specific residue (a water
> molecule) at each frame. It is suggested that this can be done using NAMD
> energy plugin. However, I would like to do the job through a script because
> my trajectory is in a remote server.
>
> I tried the following.
> obtained the code in this link and created a .tcl file called
> namdenergy.tcl in the folder where I have my script.
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-
> l/att-7277/namdenergy.tcl
>
> Then I wrote a different tcl script with
> source namdenergy.tcl
> namd energy -all -sel $sel -par myparameterfile.inp
>
> Here I specified the parameter file because my parameter file is different
> from the common charmm parameter file. However, I am getting the following
> error
>
> invalid command name "::FinderTool::find"
>
> I would be grateful for a guidence to correctly use the namd energy to
> calculate energies of some selected atomselections.
>
> Thank you.
> Best,
> Monika
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
>

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