VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 02 2010 - 17:00:48 CDT

On Wed, Jun 2, 2010 at 5:17 PM, ban arn <ban.arn_at_gmail.com> wrote:
> 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).

that is not an easy task. if autopsf doen't work, then you'll have to do it
the old fashioned way. there are tutorials on the subject. you also have
to make sure that you have the proper parameters for all components involved.

so you basically have to redo what you did for desmond before.

also, if you don't have the exact matching parameters in a format that
NAMD can handle, your namdenergy calculation will be a waste of your time
since the energies will not be consistent with the trajectory. you'd have to
rerun the full trajectory.

cheers,
   axel.

> 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/      Fax: 217-244-6078
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.