> Yes, this is a ligand (ATP) problem. The atoms HO-OH in the first
> phosphoreus group. The parameters to ATP are from parm94.dat.
> I have tried to do dynamics on isolated ligand having shake on,
> and that is a problem. I got the SHAKE error again on the same
> atoms:
> "Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1 1 2
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)
Why is the terminal phosphate not charged (i.e. why is the H on there)?
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?
\-/ 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Dec 19 2005 - 23:53:01 PST
