From: Anjela Manandhar (
Date: Mon Dec 01 2014 - 15:00:59 CST

I constructed .rtf files for GTP and GDP using ATP/ADP and Gua topology
files. Now, for the parameter files, I am trying to do the same using
parameter files of ATP/ADp and Gua. I found parameters for Gua. Where can I
find the parameter for ATP?
Thank you
Anjela Mannadhar

Anjela Manandhar
Graduate Student
Biochemistry Program
Graduate Center, City University of New York
365 Fifth Avenue, NY-10016, USA

On Wed, Oct 15, 2014 at 3:04 PM, Josh Vermaas <> wrote:

> 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:
> 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