[gmx-users] adding ATP parms to AMBER99

[Alexey Shvetsov]

В письме от 11 апреля 2014 14:11:09 пользователь Justin Lemkul написал:
> On 4/11/14, 1:43 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
> 
> The .rtp and .hdb files that you would need to create the topology with
> pdb2gmx appear to be available from:
> 
> http://bugzilla.gromacs.org/issues/721

Heh. Someone still use my old topology =D 

> You still need to modify ffbonded.itp and ffnonbonded.itp to use the
> published parameters, since they differ from those already in the force
> field.
> > 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.
> 
> Abort any notion of using PRODRG.  The topology is of no use to you, because
> you literally have to change everything about it.
> 
> > 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)
> If you can explain where you're stuck, probably someone can suggest
> something to help.  Without knowing what "stuck" means, there's not much to
> go on :)
> > 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.
> 
> All that's necessary is translation between file formats (and units); there
> are many scripts online floating around that do this.  Your approach (aside
> from the PRODRG tangent) is correct.
> 
> The simplest test to convince yourself that everything is OK is to do a
> single-point energy evaluation within Gromacs and then in AMBER; if the
> energies are the same, the force fields are equivalent.
> 
> -Justin

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 
Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Developer
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru