From: Axel Kohlmeyer (
Date: Sun Nov 11 2007 - 00:54:50 CST

On Sat, 10 Nov 2007, Santanu Chatterjee wrote:

SC> Hi VMD users,

hi santanu,

SC> I need to run simulations of few alkanes (pentane, hexane) etc. I
SC> have got PDB files for those. I need to generate PSF files. I was
SC> trying to find topology and parameters files for those alkanes by
SC> google. So far no luck. I was wondering if any vmd user know where to

if that fails, you can always write them yourself.
you may want to check the literature (still more
reliable than google!) for publications of special
force fields for alkanes and their parameters.

as a last line of defense, you can probably adapt
parameter files for lipids to do corresponding alkanes.
should be pretty straightforward and there should be
information on the VMD/NAMD homepages (or in the CHARMM
forums) on how to write your own parameter files.

good luck,

SC> find them. I will appreciate if someone can point me to that.
SC> Thanks,
SC> Santanu

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.