[gmx-developers] Amber ff?

[David van der Spoel]

On Mon, 2003-09-22 at 11:50, Anton Feenstra wrote:
> Erik Lindahl wrote:
> > Hi,
> > 
> > The problem is that pdb2gmx really screws things up since it has tons of 
> > things hardcoded for united atom force fields with naming exactly has 
> > gromos/gromacs. It assigns wrong hydrogen types in nucleic acids, etc.  
> > David and I have started looking into that, but I don't expect we will 
> > release it until we have a more general pdb2gmx, or rather: until we 
> > have replaced pdb2gmx with the xml code...
> 
> I got a reply from Eric Sorin, and hopefully he will give us the preliminary
> ff files. I'll see how far we can get with those and 3.x pdb2gmx... I'd think
> others would also be interested in a 3.x 'backport' Amber ff...?

The point Erik L was trying to make is that even with
perfect force field files you will not be able to make a 
correct topology with pdb2gmx, because of the inherent
assumptions in the code. We are trying to put all these
assumptions into the database files. This is not easy,
however. 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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