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dockingvina [2014/01/01 21:47]
flack [How to use]
dockingvina [2014/03/29 21:42]
rkiss
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 You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://​autodock.scripps.edu/​resources/​adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation,​ only a quick check for file validity will be performed. You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://​autodock.scripps.edu/​resources/​adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation,​ only a quick check for file validity will be performed.
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 +Please note that the PDB upload file size limit is currently 2MB. If you have a larger PDB file, we suggest to extract and upload only the binding site or a single monomer/​chain from the PDB file. You can extract monomers by any text editors. To reduce the file size, you can eliminate all lines and keep the ATOM records only. You can find the chain identifier after the three letter residue name (in the below example "​PRO"​ is the residue and "​A"​ is the chain identifier).
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 +{{:​pdbextr.png?​500|}}
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 == Binding site center == == Binding site center ==
dockingvina.txt · Last modified: 2014/03/29 21:58 by flack