ADL: ADT problem

Daniel Fernandez danfer at linuxmail.org
Wed Nov 2 07:21:59 PDT 2011


Hi Phil,

 is your protein backbone complete in the PDB file? Are there any gaps with missing peptide bonds? open the PDB file with a text editor and check the remarks...

 Hope this helps

 Daniel

----- Original Message -----
From: Cunningham, Phil
Sent: 11/02/11 01:04 PM
To: autodock at scripps.edu
Subject: ADL: ADT problem

 Hi Autodock I have a pdb file I wish to convert to pdbqt format using ADT I read in the molecule circa 4000 atoms edit misc - check missing atoms says 0 (zero) edit hydrogens add polar only edit charges add Kollman edit charges compute Gasteiger - total charges added 6.0125 edit charges check totals on residues spread charge over all atoms file write PDBQT OK ERROR Cannot create the PDBQT file, all atoms do not have an autodock_element field can anyone point to my error? both RasMol and Jmol can display / interact reasonably with the source file babel / open babel blows up in windows and is taking an eternity on ubuntu (getting nowhere) many thanks phil -- Phil Cunningham Senior Bioinformatics Officer King's College London Department of Biochemistry Franklin Wilkins Building 3.157 150 Stamford Street London W1 9NN Tel +44 (0) 20 7848 4239 ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---


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