Hi Atila,
Your molecule is relatively flexible and the default SCF and geometry convergence criteria in sqm are extremely tight. You should see this by looking at sqm.in and sqm.out. I don’t know how you optimized your geometry with Gaussian but it is still far from an AM1 optimized geometry, hence sqm will take many steps to converge. Try passing more loose criteria to antechamber, e.g. to get started
-ek "qm_theory='AM1', grms_tol=0.1, scfconv=1.d-6, ndiis_attempts=100,”
which took less than a minute on my laptop for your imt.pdb molecule. You can then play with tightening convergence criteria, although I think it will not have any significant effect on your chares. Have also a look at the bottom of page 287 of the Amber 18 manual.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Aug 3, 2018, at 8:52 AM, Atila Petrosian <atila.petrosian.gmail.com> wrote:
>
> Dear Gustavo,
>
> Thanks for your answer.
>
> I have 2 ligands. I got them from pubchem database.
>
> I optimized one of them using gaussian software. But both of them have same
> error when using antechamber.
>
> imt.pdb (with energy optimization)
>
> https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde
>
> srf.pdb (without energy optimization)
>
> https://1drv.ms/u/s!AveJH4Y30cH0sQxETzLmmhHJIY8G
>
> How to resolve it?
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Received on Fri Aug 03 2018 - 11:00:03 PDT
