Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17?

From: David A Case <>
Date: Thu, 22 Mar 2018 21:27:17 -0400

On Fri, Mar 23, 2018, Dai, Shuo wrote:
> a. This input geometry for am1bcc wasn't the output from sqm, but the
> input for sqm.

am1bcc doesn't actually use any geometry information. It applies charge
corrections based on the bonds in the molecule, but doesn't care about
the exact geometry.
> b. The mulliken charges in the sqm.out only have value for "step
> 1". Do we used this as the final result? But it is not exactly the
> same as in "ANTECHAMBER_AM1BCC_PRE.AC". Most of them are the same
> but there is one or two are different. I suppose the charge in
> "ANTECHAMBER_AM1BCC_PRE.AC" should come from the mulliken charges in
> sqm.out. But the fact that sqm.out only contains mulliken charge for
> "step 1" makes me confused.

I'm not sure why it says "step 1" in the sqm.out file. These look like
charges after geometry minimization. You could check this by running
an sqm run with no optimization, and seeing what you get.

> c. In the the keyword are "AM1,
> grms_tol=0.005 ... etc". there is a python script in
> "/opt/anaconda/lib/python3.6/site-packages/pymsmt/mol/" that
> was installed by ambertools. In this script, the section "write sqm
> input file", it reads "print(" qm_theory='PM6', grms_tol=0.0002,",
> file=sqm_scf)". So my question is, why these two are different? Is this
> not intended for antechamber workflow?

The indeed has nothing to do with antechamber. pymsmst is for
metal ions, and uses PM6 (rather than AM1), etc.


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Received on Thu Mar 22 2018 - 18:30:03 PDT
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