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Hi all,<br />
<br />
I have been having issues with my system blowing up due to bad contacts. All of these contacts have been made by me when I have tried to "dock" or align my protein with my ligand in pymol. I do what I can to limit while still having the correct geometry and also being close enough to keep waters out of the contact region. What I have found to allow md/sd to run is to anneal my system under -DPOSRES for 20 ps and from 5K to 300K in the first 10ps then hold at 300K till the end. <br />
<br />
I see no physical problem with doing this due to the restraints on my ligand and protein, what I wish to know is if this will cause artifacts in my system?<br />
<br />
Thank you,<br />
TJ Mustard<br />
mustardt@onid.orst.edu<br />
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