ADL: error in parsing pdbqt file with vina

Paola Bisignano paola.bisignano at gmail.com
Fri Mar 26 02:29:08 PDT 2010


I run mydocking with autodock 4.2 and then I want to run my docking
also with vina, by using input pdbqt file, genereted  previously with
autodock, but I had a problem with one of my ligands, STU
(staurosporine):
the error message is:


Reading input ...

Parse error on line 43 in file "STU.pdbqt": Atom 33 has not been found
in this branch


so I opened the pdbqt file and remove these lines:

BRANCH  12  33
ENDBRANCH  12  33

and then it runs

what does it mean?


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