[gmx-developers] force field reorganization

[Berk Hess]

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