From: Peter Freddolino (
Date: Sun Nov 11 2007 - 11:02:52 CST

Hi Santanu,
in addition to Axel's suggestions, you should have a look at the
"stream" directory that comes with the charmm forcefield distribution;
this directory contains many small molecules which were used as
fragments in parameterizing the complete forcefield. The file containing
protein model compounds has many alkane entries in it.

Santanu Chatterjee wrote:
> Hi VMD users,
> I need to run simulations of few alkanes (pentane, hexane) etc. I
> have got PDB files for those. I need to generate PSF files. I was
> trying to find topology and parameters files for those alkanes by
> google. So far no luck. I was wondering if any vmd user know where to
> find them. I will appreciate if someone can point me to that.
> Thanks,
> Santanu