Re: [AMBER-Developers] [AMBER] ATTN GLYCAM users: CY atom type work around

From: Scott Brozell <>
Date: Sat, 10 Dec 2011 14:41:52 -0500


Force field files are textual. So even something as trivial as
cd dat/leap/parm
grep -h '^.. ' *dat | cut -d' ' -f1 | sort | uniq | less
should go a long way towards preventing duplicate names.

Probably a more sophisticated protocol would be useful,
but force field creators should be doing simple checks like
the above as a matter of routine.


On Sat, Dec 10, 2011 at 06:26:26PM +0000, B. Lachele Foley wrote:
> We've been trying to figure out a way to bring this type naming thing up. We would like to implement some sort of new-type-generation procedure that will help keep force fields from introducing duplicate types. This doesn't matter, of course, with two similar force fields, say for proteins. But, for force fields that might get mixed, it totally matters. When we chose CY, it almost certainly wasn't being used by anyone, and that's why we chose it. But, there isn't a good way to declare that, so other folks don't know to avoid it. We were planning to suggest a procedure rather than just complain, but... we are all so very overwhelmed.
> We did check ours against the other force fields. In fact, we have a program that will check for overlap between any two force fields, so we can do it automatically. I don't recall the most recent results, but there were more of them. I'll check into how hard it will be to share the program.
> From: case []
> On Sat, Dec 10, 2011, Jodi Ann Hadden wrote:
> > Currently there is an issue with the CY atom type which overlaps in
> > ff99SB and GLYCAM.
> Thanks for looking into this. Note that ff10 and ff11r4 also have some
> new atom types for proteins. Can you check for additional name overlaps.
> (You need to switch the "ff11" branch to get ff11 parameters.)

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Received on Sat Dec 10 2011 - 12:00:03 PST
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