Re: [AMBER] problem on minimization

From: ZHAO Ruisheng <zhaoruisheng.ihep.ac.cn>
Date: Thu, 25 Sep 2014 16:09:46 +0800 (GMT+08:00)

Thank you very much. I have solved the problem. The problem stems from the inappropriate parameters.

2014-09-24 21:43:48,ZHAO Ruisheng<zhaoruisheng.ihep.ac.cn>д
> 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,
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 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 Thu Sep 25 2014 - 01:30:02 PDT
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