Re: topology/parameter entries for methane?

From: Jerome Henin (heninj_at_gmail.com)
Date: Wed Dec 17 2008 - 20:25:32 CST

Hi Sebastian,
I don't have the topology file, but in a dusty folder of my hard disk,
I did find a psf file from ancient CHARMM lore... It got passed on to
me by a shaman from my tribe who even claimed he could talk to Martin
Karplus.

It goes something like this:

       1 METH 1 METH CB CT3 -0.560000 12.0110 0
       2 METH 1 METH HB1 HA 0.140000 1.00800 0
       3 METH 1 METH HB2 HA 0.140000 1.00800 0
       4 METH 1 METH HB3 HA 0.140000 1.00800 0
       5 METH 1 METH HB4 HA 0.140000 1.00800 0

>From this, you can easily reconstruct the topology. The regular CT3
and HA alkane parameters do the trick, and you've got the charges
here. The good news is that this model has just about the right
hydration free energy, see there:
http://dx.doi.org/10.1063/1.1587119

Jerome

On Wed, Dec 17, 2008 at 7:08 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> wrote:
> Dear All,
>
> I know this has already been posted once,
> but does anybody have residue topology/parameter entries for methane?
>
> Thank You,
> Cheers,
> Sebastian
>
>

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