Why are the ligands OUTSIDE the protein?

Message boards : Docking@Home Science : Why are the ligands OUTSIDE the protein?

Author	Message
DrehPunkt Joined: Oct 13 11 Posts: 1 ID: 44744 Credit: 11,821 RAC: 0	Message 6480 - Posted 17 Oct 2011 4:14:23 UTC
	My laptop is at >80% crunching through 1ebw1hsg_mod0014crossdockinghiv1_3886_53210_0, but still I get to see this: Why is the ligand floating in the middle of nowhere, outside the protein? Seems to me it should be bound somewhere to the protein, or is there something wrong with the viewer? Coz if not, my CPU has been calculating for over 9 hours how to fit a ligand in empty space :& Hopefully, something is wrong with my computer, and noone else is having this problem, but this seems rather unlikely...
	ID: 6480 \| Rating: 0 \| rate: /

Boyu Zhang Forum moderator Project administrator Project developer Project tester Joined: May 5 10 Posts: 88 ID: 28821 Credit: 2,013,795 RAC: 0	Message 6481 - Posted 17 Oct 2011 23:42:40 UTC - in response to Message ID 6480 .
	Hi DrehPunkt, There is nothing wrong with the simulation or with your computer. There are two components about Docking@Home, 1) the docking simulation which is done by charmm that uses the cpu resource when it is idle, and 2) the screen saver which is responsible for the graphical display of the protein and ligand. And the screen saver is independent from the docking simulation. Based on the results we collect back, the simulation itself is done correctly without error, but in the screen saver, when representing the ligand and protein graphically, the centering and calibration of ligand and protein positions are designated for self-docking simulations. In the cross-docking workunits that we are distributing now, a couple of ligands (e.g 1ebwxxxx) have graphical representation errors such that the ligand is outside of the protein, but the simulation is done without error. The developer of the screen saver in our group has graduated, and I emailed him to ask about the code. I will update you if I hear back. So there is no error with the simulation, just some mis-representation in the screen saver. Thanks for volunteering! Boyu My laptop is at >80% crunching through 1ebw1hsg_mod0014crossdockinghiv1_3886_53210_0, but still I get to see this: Why is the ligand floating in the middle of nowhere, outside the protein? Seems to me it should be bound somewhere to the protein, or is there something wrong with the viewer? Coz if not, my CPU has been calculating for over 9 hours how to fit a ligand in empty space :& Hopefully, something is wrong with my computer, and noone else is having this problem, but this seems rather unlikely...
	ID: 6481 \| Rating: 0 \| rate: /

Message boards : Docking@Home Science : Why are the ligands OUTSIDE the protein?

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