Re: [AMBER] problem on minimization

From: David A Case <>
Date: Wed, 24 Sep 2014 09:43:48 -0400

On Wed, Sep 24, 2014, ZHAO Ruisheng wrote:

> I performed a minimization prior MD with a restrain on the main chain of protein, but it stopped abnormally with the following information,
> 500 -8.8367E+07 2.6492E+11 5.2269E+13 Fe1 4716
> BOND = 11384.5592 ANGLE = 630.4843 DIHED = 3017.7653
> VDWAALS = 29019.8034 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 1038.0888 1-4 EEL = 8806.2948 RESTRAINT = 125.4126
> EAMBER = *************
> Dose it means that the restrain on Fe1 is too small?

Visualization is probably your best bet here. Since you have iron atoms
in your system, you have a non-standard force field, and it will not be
possible to make any generalizations. We don't (for example) know what
the initial structure looks like (or what its energy is); nor to we have
any information about why the calculation stopped at step 500. The
problem is unlikely to be related to the restraints, but we don't know
what your restraint weight is, or which atoms it is applied to.

But it looks very much like you have a bad initial structure. Use the
"checkoverlap" command to look for bad contacts, and a visualization program
to carefully look at the structure (and to how it moves during minimization.)
Since the bad forces are at the metal center, see if you can successfully
minimize a small fragement that includes Fe1.

...good luck....dac

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Received on Wed Sep 24 2014 - 07:00:03 PDT
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