So, if you also set the qmmm_int=1 (which I guess is the default value),
you get geometry opt base on the electric field of external point charges,
is that right?
Cause then, if you have a metal ion or a deprotonated amino acid close to
the inhibitor then its charges should be different from using antechamber
where the external charges are not taking in to account. Am I right?
Thank you,
Sofia V.
> On Tue, Sep 15, 2015, Sofia Vasilakaki wrote:
>>
>> Is it possible to use sqm for geometry optimization of a ligand and use
>> the output for deriving AM1 or RESP charges in antechamber?
>
>> Saying this, what is a typical input / output file for running sqm opt
>> ?
>
> If you want to use sqm to geometry-optimize your molecule, set the
> "maxcyc"
> parameter (and maybe the "grms_tol" parameter) in the &qmmm namelist.
> See Section 9.3 of the Amber 2015 Reference Manual. There is an example
> input file in that section. Defaults for sqm will perform a geometry
> minimization with a reasonable (but not overly tight) convergence
> tolerance.
>
> ....dac
>
>
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Received on Tue Sep 15 2015 - 13:00:03 PDT
