[gmx-developers] force field reorganization

[Tsjerk Wassenaar]

Hi Berk,

Sounds like a good idea. So it would also be easy to add ligands, as
it would only require to put a ligand.rtp to the directory, without
editing the original files? But what will happen if a certain residue
is defined in different files? Will it issue a warning, or an error,
something else?


Cheers,

Tsjerk

On Mon, Jan 25, 2010 at 3:34 PM, Berk Hess <hess at cbr.su.se> wrote:
> Hi,
>
> I have made some changes in pdb2gmx to better organize all the force
> field files.
> But before I commit, I would like to have some feedback from the GROMACS
> community.
>
> If have now made it such that force fields are all in separate
> directories and there is
> no longer an FF.dat file.
> Force fields are now detected by pdb2gmx by a filename in a subdirectory
> as follows:
> <ffname>.ff/forcefield.itp
> For example for OPLS:
> oplsaa.ff/forcefield.itp
> If the directory also contains a file forcefield.doc, the first line of
> this file is assumed
> to be a short description of the force field and this is printed
> (previously this was in FF.dat).
>
> pdb2gmx then reads any files ending on .atp, .r2b, .rtp, .tdb, .hdb,
> both from the force field directory and the current working directory.
> The only mandatory files are one .atp file and one .rtp file.
> Termini from .tdb files are only applied to rtp entries from .rtp files
> with the same base file name.
> The general idea is to have, for instance:
> atomtypes.atp
> aminoacids.rtp
> aminoacids.n.tdb
> aminoacids.c.tdb
> aminoacids.hdb
> dna.rtp
> dna.n.tdb
> dna.c.tdb
> dna.hdb
>
> Especially useful for AMBER, you can have .r2b files to map residue
> names to building block names,
> depending on the protonation state and if in termini or not.
> Also useful for AMBER, you would not longer be required to make tdb files.
> pdb2gmx checks if there are no dangling bonds due to missing termini.
>
> For backward compatibility of grompp there would still be a file such as
> ffoplsaa.itp
> in the lib dir, which would simply #include ffoplsaa.ff/forcefield.itp,
> similarly there will
> be spc.itp, tip3p.tip, ions.itp etc.
>
> Are there any objections or comments?
>
> Berk
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist