Generating psf for a drug, trimethoprim

From: Charles Moad (cmoad_at_indiana.edu)
Date: Sat May 14 2005 - 18:00:08 CDT

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     I am trying to create psf files for doing a simulation via namd/
vmd. I have a protein chain, and I also have a pdb coord file for
trimethoprim (http://alpha2.bmc.uu.se/hicup/TOP/). Having a computer
science background, I am unsure how to correctly generate a psf file
for this drug. I can successfully create one for 1dfh chain a using
psfgen, but the same topology file does not work for the drug. Do I
alias TOP? Do I have to find a different topology file? I currently
have top_all27_prot_lipid.inp. Sorry if this is a simple question.

Thanks,
     Charlie

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