ADL: Setting the grid over specific residues

Lokesh P. Tripathi lokesh at
Wed Oct 10 23:40:56 PDT 2007

Dear all

I am using autodock 3.05 to perform the docking of a tryptase inhibitor
(41 amino acids in length) to a trypsin structure (native PDB stucture and
a modeller derived homology model). I have faced a few issues in this and
woudl be extremely grateful if someone could provide some clues on how to
get around these problems

1. when I select the macromolecule (for preparation) using
Grid-macromolecule-Choose...(AG3) command, I get the foloowing message
initializing xxx.pdb
it is not a peptide
-added gasteiger charges
-found 0 non-polar hydrogens
-added solvation parameters

I am not sure about the message it is not peptide. Is it because the
protein in question is over 200 residues long and so technically doesn't
qualify as a peptide? But the protein provided for test purposes too
contains 100 residues and is identified as a peptide by Autodock. Is there
any particular input format prior to preparing the PDB file by adding

2. That brings me to the next question. The file was genrated by splitting
a PDB complex into two PDB files using a text editor and thus, the two new
PDB files retain only the ATOM record for either protein. Wil this cause
any problems with autodock (such as above)?

3. The most imposratnt part. I wish to bind the inhibitor (ligand) to
enzyme active site by placing thr GRID Over the binding site region
demarcated by a set of residues say 189-192, 214-216 and 224-228. How can
I do that using ADT or through command line?

Any assistance would be most welcome

Lokesh P. Tripathi
National Centre for Biological Sciences,
Bangalore, India

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