VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Oct 15 2014 - 17:45:30 CDT
The most recent CHARMM forcefield releases at least contain explicit GTP, GDP etc. contained in stream/toppar_all36_na_nad_ppi.str. You can get the forcefield files from http://mackerell.umaryland.edu/charmm_ff.shtml - but be aware that if you’ve never done this before there’s a bit of a learning curve involved in putting them to use in NAMD. A very productive learning curve, I hasten to add...
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Josh Vermaas
Sent: Thursday, 16 October 2014 5:04 AM
To: Anjela Manandhar; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: GTP and GDP parameter files
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
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?