From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Jul 08 2004 - 09:25:13 CDT
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 above.
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.
shirley
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