Re: [AMBER-Developers] Amber atom type naming (and parms)

From: B. Lachele Foley <>
Date: Wed, 14 Dec 2011 23:23:12 +0000

Sounds ok. I worry that fragment-based parms could introduce a lot more complexity and associated entropic drift to have to contain. Otherwise, yeah, cool.

I've been tooling around with the Glycam param set to make it as orthogonal to parm99 and parm10 -- and everything else -- as possible. I still need to test more, but I think I managed to make it so the load order mostly doesn't matter in most cases.

On that subject, I could use input:

* A conflict is introduced in parm10 -- the type CP (also long unused) is being used again there. I just learned that today. I'm arguing that we should give in on this one. Not sure if I'll win.

* We changed the params in angle OS-P-OS to a value that better fits crystal structure data for nucleic acids, lipids and carbs. There is a conflicting (and older) parm set in 94/99/10. Any chance y'all might want to adopt ours?

Older one: OS-P -OS 45.0 102.60 Parm94
Ours: OS-P -OS 45.0 109.6 Parm94 and changed eqm value for better reproduction of average of crystal structures

:-) Lachele

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

From: Yong Duan []
Sent: Wednesday, December 14, 2011 5:13 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] Amber atom type naming

I talked to Junmei, Piotr and Ray. We propose,

1) Glycam will use "CY" atom type. Changes in other parts will have to be
made for consistency.
To avoid conflict:
2) Atom type of amino acids and nucleic acids will be named using two
upper case letters (e.g.: CA).
3) Atom types in GAFF will be named using two lower case letters, as is
the case now (e.g.: ca).
4) New atom types in Glycam will be named using upper case first letter
and lower case second letter (e.g.: Ca).
5) Atom types in lipids will be named using lower case first letter, upper
case second letter (e.g.: cA), the same as what Ross has done already.

In the long run, however, we need to develop a robust fragment-based
scheme. There are numerous advantages in the atom type based schemes. A
good example is the OPLS force field which is almost entirely based on
atom types. However, as the need of force field accuracy increases, the
number of atom types will inevitably grow. More importantly, some of the
critical parameters, such as partial charges, can not be reliably
parameterized using atom types. In fact, AMBER has been using a hybrid
atom type + fragment scheme. For example, the charges of nucleic acids and
amino acids are fragment-based whereas the bond parameters are atom type
based. This is also the case for glycam and lipids. We think it is time to
move fully to the fragment based approach. One clear advantage of the
fragment-based approach is the potential to develop accurate partial
charges for GAFF. However, this will take considerable effort to develop,
not least of which is the need to improve leap/gleap and the need to
develop the fragment databases. We envision that atom types will remain an
important part of the new scheme but their role will be mainly in the area
of connecting the fragments.

We also hope that this move will solve the long-standing issue of

Let us know if you have any comments.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
AMBER-Developers mailing list
AMBER-Developers mailing list
Received on Wed Dec 14 2011 - 15:30:03 PST
Custom Search