Subject: Large H-bonded complexes; freezing and activating coordinates; ONIOM

From: Roy Jensen <[email-masked]>
Date: Thu, 21 Feb 2002 22:54:36 -0800 (PST)

All

I am trying to look at hydrogen bonding in large complexes with G98. I
currently optimize the entire complex with AM1 and then use a higher
method on the atoms involved in hydrogen bonding. I am having problems
with the latter. I want to freeze all the atoms (no problem with this
step) and then selectively activate the desired atomic positions, bond
lengths, angles, and dihedral angles. A ONIOM calculation on the final
complex should optimize the atoms involved in hydrogen bonding at a higher
level while leaving the remaining complex frozen at the AM1 level.

Freezing is accomplished with
	* F
	* * F
	* * * F
	* * * * F

Specific atoms, bond lengths, angles, and dihedrals are activated (in the
same modredundant block) with
	2 A
	4 A
	2 * A
	4 * A
	* 2 * A
	* 4 * A
	* 2 4 * A
assuming atoms 2 and 4 need to be activated.

The output file shows that the appropriate parameters are being optimized.
The problem is that the job completes all steps and the final geometry is
IDENTICAL to the input geometry! I am guessing that some unprinted bond
lengths, angles, and dihedrals are still frozen, preventing motion of
these atoms. I have tried removing (R) and killing (K) all the parameters
instead of freezing (F) them. Both of these fail immediately with an
'Incomplete coordinate system.' error.

Any suggestions would be appreciated.

Is there another way to go about this?

Roy Jensen