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

From: B. Lachele Foley <>
Date: Sat, 10 Dec 2011 18:26:26 +0000

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.

Yeah, will fix the repo. Actually, we have a version h poised to pounce, too. We still haven't made tleap tests, either. Sigh.

Oh.... last I recall... it works because... and I might have some of this backwards, but essentially: Leap takes the first atom type assignment but the last force field parameter assignment. So, we load leaprc for our stuff to set the atom types. Duplicate types in 99SB get ignored, but the params from SB overwrite ours. So, we reload our leaprc to set the params right, without affecting the types, which are all ignored.

Got that info from observed behavior, not from inspecting code.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: case []
Sent: Saturday, December 10, 2011 9:24 AM
Subject: Re: [AMBER-Developers] [AMBER] ATTN GLYCAM users: CY atom type work around

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.)

> - Go to and download the most up-to-date version
> of the parameters.

It looks like Glycam_06g-1.dat is slightly different from the corresonding
file (GLYCAM-06g.dat) in the git repo. Can you bring the latter up to
date, probably putting the full id in the header line, removing references
to "Amber 8" etc.

> - If you are building a system that contains a carbohydrate, load
> GLYCAM, ff99SB, then GLYCAM again.
> source leaprc.GLYCAM_06
> source leaprc.ff99SB
> source leaprc.GLYCAM_06

Can you explain why this works? Is there a fix going forward that eliminates
the need for this workaround?


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Received on Sat Dec 10 2011 - 10:30:02 PST
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