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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Tue Feb 19, 2013 2:31 am 
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That is difficult to answer. But here I go: it is a waste of computational time to go beyond 1000 steps of steepest descent because the structure won't improve after that and it might even degrade a bit. GC is completely overkill unless you are planing on running molecular dynamics. As for the effects on docking, all I can say is that in my hands those 1000 SD steps make all the difference when doing the docking.

Now, you have seen that I recovered the XRD structure, so you need to find the right workflow to reproduce it. Once you standardize that, you are golden.

Good luck!


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PostPosted: Wed Feb 20, 2013 2:21 am 
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Hi LK,

After trying 6 different runs without much luck (varied steps/SD/CG/no CG, etc) I finally gave in and attempted just to minimise the structure using OPLS2005 in Maestro - exporting this minimised structure docked with vina perfectly!

I will stop bugging you now as I have enough hope to keep hammering away at Amber/Chimera until it works, but I was just wondering - did you use the default ff12SB forcefield? I can only think of that being the last difference, either that, or pure luck in the minimized structure's trajectories being suitable for vina to dock the ligand correctly. And i'd rather rule out luck at this point!

Also could you please private message me some of your details so I can include you in acknowledgements in my thesis for the assistance you have provided so far (if you are comfortable with this).

Sebastian


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PostPosted: Sat Feb 23, 2013 12:33 am 
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BTW, send me a copy of your thesis (PDF is fine) when it is available, ok?
:D


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