[gmx-developers] Amber ff?
lindahl at stanford.edu
Mon Sep 22 18:12:08 CEST 2003
Guha saw Anton's first post, and Eric said he wouldn't mind if people
tested it. However, be aware that you need to change things manually in
the topology, and check atom types and dihedrals carefully - the
released pdb2gmx used to remove stuff that shouldn't be, and change
I told him Anton might volunteer to fix the termini databases if you
got access to it :-)
Still, though - keep in mind that it's not for general consumption
On Monday, September 22, 2003, at 03:50 AM, David van der Spoel wrote:
> On Mon, 2003-09-22 at 11:50, Anton Feenstra wrote:
>> Erik Lindahl wrote:
>>> 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,
>>> David and I have started looking into that, but I don't expect we
>>> 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
>> 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,
> 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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