VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Oct 15 2014 - 14:04:06 CDT

Hi Anjela,

I believe the accepted solution in the CHARMM force field is to combine
the nucleic acid topology (top_all36_na.rtf for the guanosine) with a
patch to make it into GDP or GTP. I found the patch (5DP) for a
diphospate to the base in stream/na/toppar_all36_na_nad_ppi.str, but I
didn't see one to add a triphosphate on. You can build the patch fairly
easily yourself by borrowing charges and atomtypes for the triphosphate
group from the ATP residue and following the logic of the diphosphate
patch. If you need help reading the topology file, there is a tutorial
for that which covers the basics:
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/topology-tutorial.html

With the patch in hand, you could make your GDP/GTP residue by first
renaming it to guanine and then adding the patch on (see the psfgen
userguide). If you wanted to make a GDP, this is what your patch
statement would look like (assuming the GUA is residue 1 of segment G):

patch 5DP G:1

Good luck!
-Josh Vermaas
On 10/15/2014 10:02 AM, Anjela Manandhar wrote:
> I need to simulate a protein with GTP and GDP in it. I could not find
> the parameter files for GTP and GDP. Do I need to build one? If yes,
> how can I do that?
>
> Thanks
> Anjela Manandhar
>