[gmx-developers] force field reorganization

[Justin A. Lemkul]

I assume it will also still be relatively easy to implement new force fields? 
In the past, it was as easy as copying the necessary files to $GMXLIB and 
updating FF.dat.  Now I assume one can simply add a new <something>.ff directory 
containing all the appropriate files and pdb2gmx can process them?

-Justin

Berk Hess wrote:
> Ah, good that you mention this.
> I thought about this, but forgot about it.
> I will add a check such that is always uses the first entry and warns you
> when it ignores are second one.
> Your working dir will always be read first.
> 
> Another feature is that you can now have different bonded settings
> (bond, angle, dihedral types, nrexcl, etc.) for rtp entries in different
> files.
> But within each moleculetype only one setting can be used, pdb2gmx
> checks this.
> 
> Berk
> 
> Tsjerk Wassenaar wrote:
>> 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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>>> gmx-developers at gromacs.org
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>>>
>>>     
>>
>>
>>   
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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