On Thu, Jul 9, 2015 at 5:34 AM, Clavel <dclavel.ibs.fr> wrote:
> Hello everyone,
>
> I am currently computing van der Waals interaction energy within a large
> set of residues from a MD simulation.
> I wrote a script for computing the vdW interaction energies by using the
> namdenergy plugin that is looking like:
>
> > package require namdenergy
> > set res58 [atomselect top "protein resid 58"]
> > set res61 [atomselect top "protein resid 61"]
> > set output [open 2_A.dat w]
> > set nf [molinfo top get numframes]
> > set namdvdw [ namdenergy -vdw -sel $res58 $res61 -cutoff 12
> -ofile 2_A.dat]]
> > puts $output " sim #: _A "
> > close $output
> > $res58 delete
> > $res61 delete
>
> However, $res61 is a non standard amino acid. I have done my MD
> simulation with a specific force field for such residue.
>
> I would like to know how to use namdenergy plugin with a specific force
> field because so far the plugin is not able to compute the vdW
> interaction energy with my script.
>
I think you have the wrong list here. You should ask on the VMD mailing
list where this is most applicable. See
http://www.ks.uiuc.edu/Research/vmd/mailing_list/
People on this list would likely just use sander to compute energy
components if they needed it for each snapshot of a trajectory.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 09 2015 - 05:30:03 PDT
