RE: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency

From: Ross Walker <>
Date: Tue, 30 Mar 2010 14:10:45 -0700

Hi Dmitry,

> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: Job will continue with unconverged SCF. Warning energies
> QMMM: and forces for this step will not be accurate.
> QMMM: E = -0.8502E+06 DeltaE = 0.1024E-07 DeltaP = 0.2569E-08
> QMMM: Smallest DeltaE = 0.1013E-07 DeltaP = 0.2645E-08 Step =

> Protein-ligand complex is based on crystallographic structure, thus, i
> believe that starting conformation is good.

If only that were true. Often crystal structures are very poor resolution,
have errors and or guesses in certain parts of the structures and lack
protons. Net result is that even a 'good' crystal structure can represent a
bad starting geometry. I would start by followings Bud's advice. Minimize
and run some MD first classically to let the system relax. Then try turning
on the QM and see if the problem persists.

> I've tried cut off 8, 9, 10; AM1 and PM3; SHAKE and NOSHAKE
> minimization. Example of input file is attached.

It is also possible that your QM region is a poor choice, perhaps there are
link atoms across inappropriate bonds, cutting a peptide backbone for
example. You may also have the charge for your ligand set incorrectly
forcing it into some high energy state.

Note, though that SCF got close to convergence:

> QMMM: Smallest DeltaE = 0.1013E-07 DeltaP = 0.2645E-08 Step =

The default limit is 1.0 x 10^-8 on energy and it got to 1.013 x 10^-8 so it
was REAL close. You could try running the initial part of your heating /
equilibration with scfconv=1.0e-7. This will not give as good forces but may
be enough to get you away from a high energy starting structure and then you
can tighten the convergence back up again later.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Tue Mar 30 2010 - 14:30:03 PDT
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