Re: Calculate energy of a residue using NAMD energy

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Jan 30 2018 - 09:18:44 CST

Are you running this with VMD?

The Tcl environments for VMD and NAMD are different - if using NAMD my
guess is that none of those "package require" commands are working
correctly.

It requires some modest scripting, but I believe you can do what you want
in NAMD using the pairInteraction keyword (user guide p. 222) along with
the coorFile (which probably deserves more bold documentation, user guide
p. 18).

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.
>

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:19:35 CST