[gmx-users] adding ATP parms to AMBER99

[Stephen N. Floor]

Yes indeed - and thanks to Alexey and Tom for the .rtp/hdb and .itp files, respectively!  Much appreciated. 

On Apr 12, 2014, at 1:18 AM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru> wrote:

> 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
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