[gmx-developers] force field reorganization done

[David van der Spoel]

On 1/27/10 2:03 PM, Berk Hess wrote:
> Hi,
>
> I have committed the force field reorganization code and all the force
> field files to git master.
>
> If anyone wants to test, please go ahead and give feedback.
> This is a critical part of GROMACS and should be well tested.
>
> The only thing missing, I think, is updating the Makefile.am in
> share.top and adding ones
> in the .ff subdirs.

I've just updated and added stuff to the Makefile.am, now at least one 
can install gromacs. A test with the OPLS ff works, however with encads 
I get:
Atom type opls_135 (residue ACE) not found in atomtype database

The fact that ACE is not in the database does not concern me, but the 
ref to opls_135 is weird. In the encads.ff files there is no mention of 
opls_135 in any file.

> Also the manual still needs to be updated.
>
> Now we can add the AMBER and CHARMM force fields with proper building block
> naming support and support for renaming terminal building blocks.
>
> I am still thinking if it would be useful to be able to keep the
> "proper" residue names
> and not replace them by the building block names. This might not be very
> useful,
> because you can no longer easily see the protonation state or special
> bonds of residues.

In the context of qhop-development we are thinking of having all protons 
on all residues (e.g. two H on a GLU sidechain) and store an existence 
function in the occupancy field of the pdb. Maybe this should not be 
done in general, but some feedback on the idea would be appreciated.


>
> Berk
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se