Dear Syed,
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.6263E+14 2.5407E+13 6.7020E+15 HA 5145
>
> BOND = 10249.1760 ANGLE = 8398.2899 DIHED =
5699.4820
> VDWAALS = ************* EEL = -282279.1775 HBOND =
0.0000
> 1-4 VDW = 394659.2423 1-4 EEL = 28526.4465 RESTRAINT =
0.0000
The *'s mean the value is too big to fit in the space allocated for it in
the output file. This means your VDW energy is huge. In addition your forces
are massive. GMAX is the maximum gradient and here it is 6.7 x 10^15
KCal/Mol/A. Thus your initial structure is very bad - most likely you have
one or more atoms sitting on top of each other - you will need to inspect
your initial structure. In particular take a look at the region around atom
5145 since this is the one with the largest force on it.
Good luck.
Ross
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|\oss Walker
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Syed Tarique Moin
> Sent: Tuesday, August 07, 2007 06:12
> To: amber.scripps.edu
> Subject: AMBER: Problem with minimization
>
> Hello,
>
> I am facing the problem with minimizing the protein
> but it stops.
>
> i am also attaching the output file of my sander
> output.
>
> Suggest me what is the solution.
>
> Regards
>
> Syed Tarique Moin,
> Junior Research Fellow,
> H.E.J. Research Institute of Chemistry,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75720, Pakistan
>
> tarisyed.yahoo.com
> tarisyed.hotmail.com
>
>
>
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Received on Wed Aug 08 2007 - 06:07:38 PDT
