working with non-protein files

From: Adam Fraser (
Date: Mon Jun 25 2007 - 21:57:31 CDT

Hello, my name is Adam,

I'm doing some research with hydrocarbons that requires MD simulation.
 The molecule of interest is Hexadecane (C16H34). So far my
experience is limited. I've only done a handful of experiments with
small polypeptide chains. So I've been looking around quite a bit for
tutorials and documentation on how to go about preparing and
conducting this sort of simulation, but have been coming up pretty

So far I have created a pdb file of Hexadecane that I've been able to
successfully view in VMD and calculate Hydrogen positions using one of
its modelling tools.

What I'm trying to do now is generate a psf file. It looks like the
best way to do this might be to create my own topology file for atoms
in Hexadecane.... still I'm sure there's an easier way, and I was
wondering if anyone has any suggestions?

For example, is it possible to modify my pdb file so I can use the
top_all22 topology file to generate my psf?

Any input would be greatly appreciated!

Thanks very much.

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