Subject: parm94 and glycam93 in AMBER

From: Bernd Kallies <[email-masked]>
Date: Thu, 30 Apr 1998 14:45:25 +0200

We are currently dealing with molecular mechanics calculations on
proteins coupled with oligosaccharides. We decided to use an AMBER force
field together with GLYCAM. The original GLYCAM paper (Woods et al, JPC
1995) said that this parameter set (called glycam93 in the AMBER
program) was developed in agreement with the old AMBER force field
(Weiner et al, JACS 1984, called parm91), but it might also be used with
the new developed AMBER parameters (Cornell et al, JACS 1995, called
parm94) because of the similar philosophy of assignment of atomic
charges (both parm94 and glycam93 use RESP charges from HF/6-31G*,
whereas parm91 used HF/STO-3G).
Regarding to the coupling of glycam93 and parm94 we have several
questions:
1. Does anybody know if these parameter sets should be coupled in
principle?
2. If one can do so, which scaling factor of 1-4 nonbonding interactions
should be used (0.5 as for parm91 and as used in Woods' paper for
parameterization, or 0.83 as for parm94)?
3. The Woods paper refers to some parameters in the GLYCAM force field
which were adopted from the parm91 parameter set. Should these
parameters be used from parm91 also for the coupling with the parm94 set
or should they be replaced by the new parm94 parameters, which are a bit
different?

Thank you for your assistance.

Bernd Kallies

--
Dr. Bernd Kallies
University Potsdam
Institute for Physical and Theoretical Chemistry
Am Neuen Palais 10
14469 Potsdam
GERMANY
e-mail: [email-masked]
WWW   : http://www.chem.uni-potsdam.de/~kallies/kallies.htm
Tel   : [+49] (0)331 / 977-1313
Fax   : [+49] (0)331 / 977-1315