From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Wed Aug 03 2005 - 15:12:40 CDT
I am using NAMD for sampling of proteins for a
while. I need to use NAMD to do sampling for drug-like
small molecules with aromatic bonds. I have the pdb
files. But I do not know how to generate psf files.
Psfgen can not work since it can not recognize the
residue types ( which is not present at all ). Is
there any way to generate psf files for non-proteins?
Otherwise how can I do sampling simulations on
non-proteins? Also, how to get the parameter files for
these type of molecules?
I am absolutely stuck and so I would highly
appreciate any tips, suggestions in this matter.
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