AMBER Archive (2005)

Subject: Re: AMBER: MD problems/shake

From: blakrose_at_gazeta.pl
Date: Mon Dec 19 2005 - 16:45:43 CST

Dear Professor!
 
Thank you for anwsering my mail.
 
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
 
     Note: This is usually a symptom of some deeper
     problem with the energetics of the system."
 
What I can do about the problem?
 
Many thanks in advance
|\
|/
|awel Gruszczynski
 
 
>IF this is occurring in the ligand-- and it looks OK-- perhaps
you have
>force constants for the bonds that are too large? How did you
get the
>parameters for your ligand and can you run the ligand alone
(without
>water but with SHAKE on)? If you can run the isolated ligand,
make sure
>minimization of the entire complex was done prior to MD and that
there are
>no overlapping atoms (which may not be visible when you view the
structure).
 
You can follow up with more specific questions to me if need be.
 
\-/ 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_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham
 
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