ADL: Repairing a receptor prior to docking

Danny Tuckwell DTuckwell at f2g.com
Mon Mar 10 07:06:08 PDT 2008


Dear All,

            I am having problems which I think are due to inadequate
preparation of my receptor, though I am not sure. When I get to the
stage of reading in my rigid.pdbqt file (exercise 8 in the ADT4
handbook) I get an error message about non-integral charge. The residues
that are given are the N- and C-terminus, four residues that span two
breaks in the structure,and the residues that are specified in the
flexible.pdbqt file (I put hydrogens on the .pdb before I started the
docking procedure).

            Are these errors important? How can I repair the N- and C-
termini and the internal breaks, and why is ADT4 telling me that the
residues in the flex file are incomplete?

            Thanks,

                        Danny

 


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