Re: [AMBER-Developers] [AMBER] Issues with hydrogens using glycam force field in Amber 10

From: B. Lachele Foley <>
Date: Mon, 20 Feb 2012 16:41:43 +0000

I just ran the simulation. The behaviours of the hydrogens seem normal to me, but I'll ask more about what "a lot" means. The simulation is attempting dynamics in implicit solvent, so, of course, everything is much freer to move than when there are waters in the way. But, basically looks ok.

There is one odd thing -- the entire molecule "jumps" every so often. Is this an update when translation and/or rotation of the COM is removed?

:-) Lachele

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

From: David A Case []
Sent: Monday, February 20, 2012 9:13 AM
To: AMBER Mailing List
Subject: Re: [AMBER-Developers] [AMBER] Issues with hydrogens using glycam force field in Amber 10

On Sat, Feb 18, 2012, Karl N. Kirschner wrote:
> I have encountered a similar problem recently, I don't think it
> involves the glycam06g force field directly, but something with how
> xleap (didn't try tleap) interprets the force field when sourcing the
> protein/dna force field. If you look at the output structure of leap,
> I think you will see that a few of the hydrogen atoms are incorrectly
> placed. I corrected this by only loading glycam06 parameters and
> suppressing the the protein force field loading (i.e. xleap -s -f
> This then gave me the correct spatial structure of the
> carbohydrate.

Hi Karl:

Thanks for the info. Can you post a specific example? We need to track this
down. If LEaP is actually adding hydrogens in incorrect ways, it should be
fixed. (I doubt that there is any difference between tleap and xleap, since
most of their code is shared.)

Are there other codes that are more reliable in adding hydrogens to
carbohydrates? "Reduce" does a good job for proteins, but I doubt(?) that any
third-party program would know about all the atom and residue names used by
GLYCAM. Either you or someone else might check sleap, since it would be
helpful to know if the latter worked better than tleap/xleap.


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