[gmx-users] adding ATP parms to AMBER99

Thomas Piggot t.piggot at soton.ac.uk
Fri Apr 11 21:18:55 CEST 2014


Hi,

I have an itp. I will send it to you off list.

Cheers

Tom

On 04/11/2014 06:43 PM, Stephen N. Floor wrote:
> Hi gromacs users -
>
> I am trying to simulate a protein-ATP complex and am trying to add parameters for ATP to the forcefield amber99sb-ildn.  First off, I find it likely that someone has already done this - is there an .itp file for ATP floating around somewhere with the recommended parameters from Meagher, Redman & Carlson, JCC (2003)?  http://www.ncbi.nlm.nih.gov/pubmed/12759902
>
> If not, I am trying to decide between using parms generated from PRODRG (which spits out a .itp, albeit with non-amber atom types) versus editing the ffbonded and ffnonbonded files for the forcefield to include bond, angle, and dihedral parms from Meagher 2003.  Any thoughts on this?  I am partial to using parameters from Meagher 2003 since they did a full QM treatment of the ligand and these are recommended by Bryce.
>
> I tried to follow previous messages in the gmx-users list on this topic, but am stuck translating dihedrals from the AMBER94 FRCMOD file to ffbonded.itp, as recommended in a previous thread (http://gromacs.5086.x6.nabble.com/Re-AMBER-force-fields-for-ATP-td4440113.html)  For the AMBER94 PREP and FRCMOD files please see here: http://www.pharmacy.manchester.ac.uk/bryce/amber/
>
> I think I could generate input files that would be properly parsed, but am looking for verification that I'm doing it correctly before conducting simulations with incorrect parameters.
>
> Thanks for your time.
> -Stephen
>
> --
> Stephen N. Floor
> HHMI Fellow of the Helen Hay Whitney Foundation
> Doudna Group
> http://doudna.berkeley.edu
>

-- 
Dr Thomas Piggot
University of Southampton, UK.



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