AMBER Archive (2006)

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

From: Jason K (
Date: Wed Jan 18 2006 - 12:12:16 CST

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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