Re: [AMBER] Antechamber + SQM/DFTB

From: Edgar Mixcoha <>
Date: Mon, 1 Oct 2012 15:56:52 +0200

Thank you very much...

Actually in -ek flag you can put all qmmm calculation flags that sqm uses:

antechamber -i file.pdb -fi pdb -o file.mol2 -fo mol2 -ek
'qm_theory="DFTB", tight_p_conv=1, scfconv=1.d-10, grms_tol=0.0002,'
-c mul

Now it seem is working very well.

Thanks again!

2012/10/1 David A Case <>:
> On Mon, Oct 01, 2012, Edgar Mixcoha wrote:
>> I am a new user of antechamber. I have read many manuals and examples
>> to parametrize organic molecules with antechamber. I have installed
>> AmberTools 12, because antechamber is distributed with it.
>> In the beggining I don't have any problem to create files and to run
>> sqm, actually I asked for the DFTB Slater-Koster files to run sqm at
>> DFTB level, I have not been able to find an antechamber flag to calculate the
>> atom charges using that method. So, I generate with
>> antechamber and manually I
>> must change AM1 to DFTB in 'qm_theory=' flag. In fact, the calculation
>> finish well. However, I don't know how to use antechamber or any
>> command to generate a mol2 or frcmod file using that calculation
>> (sqm.out)
>> Does exist any command to say directly to sqm calculate in DFTB level?
>> What can I do to obtain coordinates and changes from sqm.out file?
> I think(?) you can us the "-ek" flag to tell antechamber to modify the keywords
> it sends to sqm, and then use the "-c mul" flag to extract the Mulliken
> charges from the sqm.out file. Worth a try. If you already have the sqm.out
> file, you should be able to run antechamber with the "-fi sqmout" and "-c mul"
> flags to read in the Mulliken charges.
> ....dac
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Edgar Mixcoha PhD
Applied Physics Departament
University of Santiago de Compostela
Soft Mater and Molecular Biophysics Group <>
Web page <>
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Received on Mon Oct 01 2012 - 07:00:03 PDT
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