.psf and .params files for IMD

From: Harit Jani (s2117034_at_student.rmit.edu.au)
Date: Wed Dec 10 2003 - 19:08:54 CST

Dear NAMD 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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