VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 02 2010 - 12:54:57 CDT

Hi,
  I don't understand what you mean when you say below:
"However it failed to assume the dafault parameter file (.psf)"

Do you have a PSF file for your structure? You will need one
in order to use these tools.

I also didn't understand what you meant when you said:
"I can able to generate xsc file."

You do have a .xsc file, or not?

I don't know much about Desmond, so it's not immediately clear
to me how workable using the output of Desmond as input into
the NAMDEnergy tool will be, but assuming you have the various
files that are required, it might actually work out.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 02, 2010 at 05:35:57PM +0100, ban arn wrote:
> Dear John
>
> Thanks for reply.
>
> Sorry for not expalining the question properly.
>
> I have used Desmond for my simulation and for analysis i'm using VMD.
>
> I have tried to run the plug-in after loading the complex with
> trajectories.
>
> However it failed to assume the dafault parameter file (.psf)
>
> I can able to generate xsc file.
>
> Kindly advice.
>
> Many Thanks
> Balaji
>
> On Wed, Jun 2, 2010 at 5:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> You can either do this with the "NAMDEnergy" plugin, or by running
> NAMD manually with the right config file etc:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 02, 2010 at 01:29:38PM +0100, ban arn wrote:
> > Hi All,
> >
> > I would like to calculate interaction energy of protein and ligand
> over
> > trajectories.
> >
> > Can anyone suggest me is there any script available for doing the
> same in
> > VMD.
> >
> > Many Thanks
> > Balaji
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078