Dear Professor!
>You state these are parameters from parm94.dat, but to my
>knowledge the standard Cornell et al. (parm94) force field does
>not come with a ATP molecule. Where did you get the topology
>definition for the tri-phosphate? Did you use the contributed
>parameters database of Bryce?(http://pharmacy.man.ac.uk/amber)
I made an ATP analog by my self with MOLDEN. Than I calculated
charges, and to do minimisation and dynamics with AMBER I used
parm94.dat. I know there are any parameters for ATP, but there are
similar once.
>Why is the terminal phosphate not charged (i.e. why is the H on
there)?
This is an kinase inhibitor proposed by SHAH et al.
>Assuming you intend to have the hydroxyl (rather than PO3-),
>what are the bond parameters for that HO and does the HO overlap
>with the OH?
Bond parameters for HO are:
HO-OH 553.0 0.960
\-/ Thomas E. Cheatham, III (Assistant Professor) College of
Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm.
Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance
Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT
84112
-/-
/-\ tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
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Received on Tue Dec 20 2005 - 00:53:01 PST
