From: ban arn (ban.arn_at_gmail.com)
Date: Wed Jun 02 2010 - 16:17:14 CDT

Dear Jonh

Let me explain you clearly.

After loading the desmond trajectory files in vmd, i save only protein and
ligand complex (as initial pdb as trajectory one and rest of the trajectory
files as gromas .trr file).

Then using these files (initial pdb and trajectory files) i would like to
calculate interaction energy using NAMD plugin.

However, I could n't able to generate .psf file (for my initial pdb) using
automated psf generator.

But i can able to generate xsc file in the plugin itself.

Kindly advice how could i generate .psf file for protien and ligand complex
(initial pdb).

Many Thanks
Balaji

On Wed, Jun 2, 2010 at 6:54 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>