VMD-L Mailing List

From: Harit Jani (s2117034_at_student.rmit.edu.au)
Date: Thu Dec 11 2003 - 18:09:52 CST

Dear John,

Thank You.

Now I came to know about PSF generation. But to do that I need to have topology and parameter files.

Can I use any of the these files? MY MOLECULE IS IPERDION WHICH NOT A PROTEIN

The Second Paragraph at :
http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-namd-tutorial/namd-tutorial-html/node22.html

“The current versions of the CHARMM forcefield are CHARMM22 for proteins and CHARMM27 for lipids and nucleic acids. The individual topology files are named, respectively, top_all22_prot.inp, top_all27_lipid.inp, and top_all27_na.inp.”

Is these file are general for all or I need to write it down for my particular molecule?

Thank You,

Yours truly,

Harit Jani.

-----Original Message-----
From: John Stone <johns_at_ks.uiuc.edu>
To: Harit Jani <s2117034_at_student.rmit.edu.au>
Date: Thu, 11 Dec 2003 10:15:30 -0600
Subject: Re: vmd-l: .psf and .params files for IMD

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.
>
>
> 

-- 
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