From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Thu Jul 08 2004 - 11:01:54 CDT
You should check your starting structure very carefully. I suppose you had to
guess coordinates for some hydrogen atoms. If that failed for some of them,
it may have resulted in superimposed atoms that would be the source of your
Le Jeudi 8 Juillet 2004 16:25, Shirley Hui a écrit :
> I am trying to run a simulation on the L chain of the protein 1CPC (that is
> the pdb code). I "think" I have set everything up correctly, however, when
> I run the simulation there are some things that I am a bit concerned about:
> 1) I get a warning : Warning: Not all atoms have unique coordinates. (see
> second line of output below). This warning appears at each step in the
> console when the energies are outputted.
> 2) When I start the minimization process the energies values show up as
> 99999999.9999 (see output below). I believe this is because of the warning
> TCL: Minimizing for 500 steps
> Warning: Not all atoms have unique coordinates.
> PRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19 8.37347e+22
> 1.063 89e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> GPRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19 8.37347e+22
> 1.06 389e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 0 966810.4900 404837.2614 2875.3521 77388.4504
> 99999999.9999 99999999.9999 0.0000 0.0000 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000
> 99999999.9999 99999999.9999 13.1080 99999999.9999 99999999.9999
> So my question is why I am getting those warnings (that not all the atoms
> have unique coordinates?) This is obviously wrong but I wonder where I went
> wrong? Would it have been when I generated the PSF structure? Maybe my
> config file is wrong? I'm not really sure where to start to figure out what
> is wrong...
> I have attached my config file.
> thanks for any insight.
-- Jérôme Hénin Equipe Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-lès-Nancy Cedex Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/
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