Re: [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain

From: David A Case <>
Date: Wed, 13 Jul 2011 14:10:44 -0400

On Wed, Jul 13, 2011, Erin Kelly wrote:
[posted a pdb file for coA]

OK: I've looked at this, and sqm indeed has trouble with this structure.
We've seen this before for some other structures: systems with a bad, but not
impossible, starting geometry, sometimes won't converge with sqm. I haven't
tried tweaking the convergence parameters that are available, however.

On the other hand, good old Gaussian seems to have no trouble with this, and
optimizes the geometry. If one then takes that geometry and feeds it to sqm,
sqm has no problems. So: sqm needs some work on convergence. However,
antehcamber also (for other reasons) needs pretty good starting geometries --
it's just hard to say what "pretty good" means in this context.

I'm attaching two sqm input files:, derived from the so-so geometry
that Erin came up with; and, which uses the Gaussian-optimized

Erin can paste the "g09" coordinates back in to a pdb file, and should be able
to get antechamber going from those.

Amber-developers might want to see if they can find out how to fix the problem
with the "" file.


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Received on Wed Jul 13 2011 - 11:30:02 PDT
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