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PostPosted: Mon Aug 06, 2012 7:47 pm 
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I thought this would be easy-

babel myligand.pdf myligand.pdbqt -xr -xp

for a rigid ligand. I am starting with pdb files that have had hydrogens added.

I am using Babel 2.3.1 Jul 31 2012.

Here are some observations-

1. Chain ids are always renamed 'A'. This is a problem when making the pdbqt file of a protein dimer, as the A and B chains both become A and you get pairs of residues with the same chain and residue id, but different coordinates.

2. Atoms are reordered so that all the atoms of a given residue are not contiguous in the file. It looks to me like this can give autogrid troubles (thinks O atoms have no bonds)

3. I thought the p option would preserve atom ids, it doesn't.

Can anyone who has used Babel for the pdbqt file generation relate how they got a usable result? It doesn't seem like it should be hard, but I have no idea what I am missing.

I have been having trouble running AutoDock and my feeling is that it might be directly related to the quality of the pdbqt files.


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PostPosted: Wed Aug 15, 2012 10:11 pm 
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I couldn't get Babel to convert to pdbqt, and I don't think it can.
Can check a post I put up earlier describing what I did.

viewtopic.php?f=27&t=2030

Hope it helps


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