Re: AMBER: MD problems/shake

From: Thomas E. Cheatham, III <>
Date: Mon, 19 Dec 2005 16:40:40 -0700 (Mountain Standard Time)

> 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?

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
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Mon Dec 19 2005 - 23:53:01 PST
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