VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 11 2003 - 10:15:30 CST

Dear Harit,
  You can create PSF files using the 'psfgen' plugin in VMD, as described
in these two tutorials:
  http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-namd-tutorial/namd-tutorial-html/node6.html
  http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 11, 2003 at 12:08:02PM +1100, Harit Jani wrote:
> Dear vMD Users,
>
> I want to do IMD using VMD, NAMD, VRPN Server. I have gone through the online example at http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/
>
> It is working fine. The problem is that it required four files
>
> alanin.conf
> alanin.pdb
> alanin.params
> alanin.psf
>
> I want to do simulation for iperdion which is a small molecule and not protein.
>
> I have gone through NAMD User guide. I have .pdb file for my molecule from InsightII. As shown in User Guide, I think that I can write .conf file. But the problem is how to get .psf and .params files for my molecule?
>
> I have done search at google and found following useful links for CHARMm (http://persweb.wabash.edu/facstaff/fellers/tutorial/charmm/parmfile.html ) and X-Plor (http://atb.slac.stanford.edu/xplor/manual/htmlman.html ). But I am not able to use these information to create .psf and .params files.
>
> Is there any other way to do IMD ?
>
> Thank You,
>
> Yours truly,
> Harit Jani.
> RMIT University.
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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