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

From: Dai, Shuo <>
Date: Fri, 23 Mar 2018 08:35:00 +0000

Thank you very much for explaining!

So if I understand it right, for

Yes, I tried sqm without opt, it gave different charge. So I think I understand this part now. Thank you!

Then back to a, do the charges in "ANTECHAMBER_AM1BCC_PRE.AC" come from the mulliken charge for optimized geometry in sqm.out? But the Mulliken charges in sqm.out and charges in ANTECHAMBER_AM1BCC_PRE.AC are not the same. (please see my post in the first email.)

Since PM6/PM6-D3 is available in sqm, why not using those to replace PM3? Well, PM6 will give a better geometry, based on which the charge assignment may be better(if mulliken charge from output is used). Or the reason we didn't change the method, is because the am1bcc correction is based on PM3 results?

I have an additional question:

The input for the "bondtype" is "ANTECHAMBER_BOND_TYPE.AC0", so which program or command is used to convert *.pdb to *.AC? since the antechamber command is:

" antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2"

The input to feed antechamber is in pdb format.

Is there a one step command that I can use it to convert "sustiva_new.pdb" to generate " ANTECHAMBER_BOND_TYPE.AC0"?

And a similar step to extract/convert sqm.out to generate " ANTECHAMBER_AM1BCC_PRE.AC"?

Thank you!

-----Original Message-----
From: David A Case []
Sent: Thursday, March 22, 2018 8:27 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17?

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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