Re: [AMBER] Antechamber problem with sqm

From: David A. Case <>
Date: Mon, 15 Jul 2013 13:58:51 -0400

On Mon, Jul 15, 2013, Hunter Brown wrote:
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: E = -0.3382E+07 DeltaE = -0.1023E+04 DeltaP = 0.3590E+00
> QMMM: Smallest DeltaE = -0.3422E+00 DeltaP = 0.3227E+00 Step = 27
> Do I need to change the specified tolerances? I saw that tolerances can
> be increased in another archive message.

See Note 6 in Section 5.2 of the AmberTools13 manual.

> Also, in Chimera it is possible to save a mol2 file. Could I
> use a Chimera-produced mol2 in parmchk instead of one produced
> in Antechamber? My guess would be that I need to have an
> antechamber-produced file.

I think the answer depends exactly how you are using Chimera: if you go the
the "Amber" menu item, chimera is simply calling antechamber in the
background, and the resulting mol2 file has the GAFF atom types. Then you
could use this as input to parmchk.

If you use Chimera to generate a mol2 file without going through the Amber
menu item, you will get a mol2 file with some other set of atom types, and
you can't use that as input to parmchk.

...hope this helps...dac

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Received on Mon Jul 15 2013 - 11:00:02 PDT
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