Dear colleagues,
in my current project I have been working with AMBER 6.0. I try to
calculate the energies of binding of different orientations of a small
moelcule within a protein. Though AMBER contains a lot of parameters for
non-protein atoms, the variety of my small molecule is not entirely
covered. As I don't have enough experience to parameterize the missing
bonds, angles, and dihedrals on my own, I was thinking of taking these
from the MMFF94.
I could imagine two ways:
1. to borrow only those parameters for the small molecule, that are
missing within AMBER, applying some scaling to the force constants
2. to use the MMFF94-parameters for the entire small molecule without any
scaling, while treating the protein with the AMBER parameters
Concerning the electrostatics I intend to stay with the AMBER philosophy,
employing the RESP methodology.
At the initial stage, I'm just interested in calcualting relative
energies, i.e. rank different conformations/orientations of the same
inhibitor with a given protein conformation.
Do you think, such a strategy would be reasonable ?
Any comments are welcome.
Merry X-mas & guten Rutsch,
Christian
-----------------------------------------------------------------
Dr. Christian Pilger
Istituto di Strutturistica Chimica "Giordano Giacomello"
C.N.R. - Sezione di Trieste
Area Science Park - Basovizza
Strada Statale 14 - Km. 163.5
I-34012 Trieste/Italy
Tel.: +39+040+226881
Fax : +39+040+9221126
e-mail: cpilger_at_oc30.uni-paderborn.de
-----------------------------------------------------------------
Received on Fri Dec 22 2000 - 09:31:16 PST
