VMD-L Mailing List

From: Hassan Shallal (hshallal_at_pacific.edu)
Date: Sun May 23 2010 - 03:53:58 CDT

Dear NAMD users,
 
I am a new user of NAMD MD simulations. I know that NAMD doesn't have charmm parameter file for small molecules. I found a charmm parameter file for small molecules called top_all36_cgenff.inp (Reference: K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and A. D. Mackerell Jr., J. Comput. Chem., DOI: 10.1002/jcc.21367).
 
The problem that I have is basically in generating psf file for the small molecule using the above parameters file, here are the two scenarios that I have tried and the description of why they didn't work:
 
Scenario 1: I attempted to use VEGA software to generate an xplor PSF file of my small molecule. It gerenated the file. However this file has a problem that makes VMD unable to merge it with the protein PSF file, what is that problem? As VMD says, the PSF file doesn't have cross terms.
My question is: is there any way that I can add cross terms to this psf file and make it acceptable by VMD? what are those cross terms? I looked in NAMD user manual and psfgen manual, couldn't find clear explanation of them...
 
Scenario 2: I attempted to use VMD itself to generate the psf file of the small molecule by either issuing the corresponding commands in the TK console or using the Autopsf builder, everything seemed fine except for one little problem that blowed out the whole thing, VMD can't identify the residue name, the small molecule had a residue name of UNK, I changed that into MOL, it still didn't work..
Another question whose answer would otherwise solve the problem: how can I use a specific residue name for my small molecule that makes it recognized and then processed by VMD?
 
I totally appreciate any feedback or advice
 
Hassan Shallal
University of the Pacific
Stockton, CA 95211