AMBER Archive (2006)

Subject: RE: AMBER: A few problems on the parameterisation of a Glutamine residue

From: Ross Walker (
Date: Wed Jan 18 2006 - 12:32:25 CST

Dear Jason,
With regards to the suitability of the torsion parameters it is difficult to
tell empirically since some of the barriers and the height of the barriers
are not always obvious. What you could do is build a small test system that
encompasses the structure you want and then fit resp charges to this and
assign it the atoms types and parameters you expect. Then set up a series of
structures that represent say 15 degree increments in rotation about the
dihedral you are concerned about. Run single point energy calculation on
these structures with amber and then repeat the calculations with say
MP2/6-31G** using a QM program. You can then compare the two energy profiles
and see how similar they are.
Others may comment differently on this, e.g. I'm not sure RED does the
charge fitting but my understanding is that for the QM calculation and resp
fitting you should cap your residue with ACE and NME. You then calculate the
ESP and then during the RESP procedure you fix the charges of the ACE and
NME atoms to those defined in the original force field. In this case those
defined on page 5190 of JACS (117) 1995, 5179.
In this way your residue which sits in the middle of the ACE and NME will
end up with an integer resp charge.
I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
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From: [] On Behalf Of
Jason K
Sent: Wednesday, January 18, 2006 10:12
Subject: AMBER: A few problems on the parameterisation of a Glutamine

Dear Amber community,

I am currently trying to build a protonated in-chain glutamine residue (the
proton being situated on the nitrogen of the side-chain amide group) using
xleap, and parameterising it with ff99.

This structure contains a somewhat unusual connection of C-N3 atom types. No
force constants or equilibrium bons lengths and angles involving both these
atoms exist within the Cornell et al. 1999 force field.

Nevertheless, there are parameters within GAFF for the (presumeably similar)
c-n4 atoms, as far as bond and angle parameters are concerned; yet I failed
to find any relevant torsional terms, neither parameters for non-bonded

Torsional parameters do exist for the c2-n4 atom types however; do you
believe that they can accurately replicate the rotational profile around the
C-N3 bond in a protonated amide? Any suggestions on this subject would be
very helpful.

The second question is a general residue development issue, that is been
asked very often, but has not recieved any clear answers as yet, apart of
references to the original amber papers many of which are not freely
available to our university. So there it goes:

How can point-charges be generated for amino acid residues. In our group we
generate the atomic coordinates, do a single point calculation at a HF6-31G*
level and the follow the RESP fitting procedure. Obtaining integer charges
however is practically impossible, since the 'ends' of each residue are
usually capped with e.g. methyl groups, which are then deleted from the
final structure. Is there a way to overcome this problem and obtain integer
charges? How can the amino acids within the AMBER force fields have overall
integer charges?
(Representing an in-chain residue as a free radical can do this, but it
gives very unsatisfactory point charges, if compared to the residues
supplied within AMBER).

Your advice will be greatly appreciated,

Jason Kalapothakis
The University of Edinburgh
School of Chemistry
Joseph Black Building, Kings Buildings
West Mains Road
Edinburgh EH9 3JJ

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