AMBER Archive (1999)

Subject: AMBER FF in Gaussian98

From: James Duncan (duncan_at_lclark.edu)
Date: Wed Jul 07 1999 - 23:43:45 CDT

Hello,

I am a novice AMBER Force Field user so please bear with me! (My prior
experience with computations is on small molecules using Ab Initio
methods--mostly CASSCF and CASPT2.)

I wish to obtain a good starting structure for an 11-mer duplex DNA
(sequence 5'-TATCGCCGAGA and its complement) to which to add lesions and
then study the resulting DNA-adduct conformations using a QM/MM method.
So far, to get my feet wet, I have tried to optimize this 11-mer duplex
with the AMBER Force Field implemented in Gaussian98, using a Spartan
(Wavefunction, Inc.) generated B-DNA structure for the input geometry
and using the charges found in the Kollman article (JACS, 1995, 117,
5179-5197). Unfortunately, the structure I get from this optimization is
greatly distorted; only the three most central GC pairs appear
reasonable.

Can anyone tell me if this should work? Perhaps the starting geometry is
a poor one, or the charges obtained from the above-mentioned JACS
article are no longer valid with the latest available AMBER FF. Should
it be adequate to use an AMBER FF optimization alone, or is it necessary
to employ Molecular Dynamics as well to get a satisfactory structure? I
have not (as yet anyway) purchased AMBER-5; will it be necessary to do
so to obtain satisfactory structures in this case? If the Spartan input
structure is a poor one, where can I obtain a better one?

I would really appreciate it if anyone would be able to help get me
started on this. I would especially be grateful to hear from anyone who
has had experience with the AMBER FF recently implemented in Gaussian98.

Thank you very much!

Jim Duncan
Professor & Chair
Department of Chemistry
Lewis & Clark College
Portland, OR