DOCK6 FAQ: Difference between revisions
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= Will DOCK run on an Intel cluster running MAC OSX? = | |||
We have tested DOCK on Mac OSX on Macintosh computers. We have never run it on an Intel cluster running Mac OSX per se, but I do not anticipate there being any problems. We include both installation code and testing scripts in the distribution. If you are unable to get the code to compile or pass the tests, I would recommend contacting the dock-fans listserv [http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans dock-fans] for more specific advice. (Terry Lang, Oct 22, 2007) | |||
= Will DOCK allow my protein ligand to have a flexible backbone? = | |||
With the release of DOCK 6, you can now access the majority of functionalities of the AMBER molecular dynamics simulation package, including more advanced minimization and md simulations. You *can* use this functionality to allow the entire system to be flexible. However, this amount of sampling will take an almost untenable amount of time during a DOCKing run. There are a variety of other flexibility options in between the structure ensemble generation that Brian recommended and the fully flexible simulation. If you are willing to tell me a bit more about your application, I can make some more suggestions that might be better for your system. | |||
Latest revision as of 18:47, 15 February 2014
Here is the FAQ for DOCK6
- Can DOCK6 write an info_file as DOCK4 did?
- Are critical points/spheres supported in my version of DOCK?
- How to protonate a receptor for docking?
Will DOCK run on an Intel cluster running MAC OSX?
We have tested DOCK on Mac OSX on Macintosh computers. We have never run it on an Intel cluster running Mac OSX per se, but I do not anticipate there being any problems. We include both installation code and testing scripts in the distribution. If you are unable to get the code to compile or pass the tests, I would recommend contacting the dock-fans listserv dock-fans for more specific advice. (Terry Lang, Oct 22, 2007)
Will DOCK allow my protein ligand to have a flexible backbone?
With the release of DOCK 6, you can now access the majority of functionalities of the AMBER molecular dynamics simulation package, including more advanced minimization and md simulations. You *can* use this functionality to allow the entire system to be flexible. However, this amount of sampling will take an almost untenable amount of time during a DOCKing run. There are a variety of other flexibility options in between the structure ensemble generation that Brian recommended and the fully flexible simulation. If you are willing to tell me a bit more about your application, I can make some more suggestions that might be better for your system.