[gmx-developers] additional rtp entries

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Wed Sep 28 17:06:36 CEST 2011

On Wed, 28 Sep 2011 23:03:34 +1000, Mark Abraham wrote:
> On 28/09/2011 8:29 PM, Alexey Shvetsov wrote:
>> Hi all!
>> Also why not make some common directory under $GMXDATA/top for such 
>> things as cofactors? for example amrbe99* series forcefields has 
>> compatible atom definitions for cofactors same for amber94 based ones. 
>> May be this will work for contributed cofactor topology?
> How would you make it easy for users to know that they exist and with
> which force field they should be used?
They can be in directory with name like ligands.amber99 so they can be 
included in rtp entry search while running pdb2gmx. I can made patches 
to realize so.
> The real problem is that anything in the repository has to have
> someone prepared to take responsibility for checking, documenting and
> maintaining it, and developers' time is finite. I think a
> contributions section is a good place for such content. Now users can
> clearly understand that the level of support implied is distinct, and
> a web search will find it.
Yes contribution page is good thing (and it contain some variants of 
forcefields and itps for limited set of ligands) but there should be 
easy way to include new rtp entryes in ff. Something like i mentioned 
above (e.g. directory like ligand.<ffbasename> in $GMXDATA/top or in 
current dir for pdb2gmx)
> Mark
>> On Mon, 19 Sep 2011 16:20:34 +0200, Berk Hess wrote:
>>> Hi all,
>>> We don't have a strict official policy for inclusion of rtp 
>>> building
>>> blocks in the standard
>>> share/top forcefield directories in Gromacs.
>>> One option would be to only allow "official" force field building
>>> blocks (where the definition
>>> of official is already difficult) and put everything else on the
>>> gromacs.org contributions page.
>>> I bring this up because of a contribution of ATP for AMBER on 
>>> gerrit:
>>> https://gerrit.gromacs.org/#change,98
>>> In this contribution certainly references should be added so it's
>>> clear where the parameters
>>> come from. But such contributions should be carefully checked on 
>>> correctness,
>>> but equally important, on compatibility with the force field and
>>> something like "acceptance"
>>> in the community.
>>> ATP would indeed by useful, but if it's easy to find on the
>>> contributions page that would
>>> also work.
>>> Berk

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

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