ADL: Could anyone help me please??

Stefano Forli forli at
Fri Nov 18 14:33:27 PST 2011

Hi Normandé,

I agree with Mihaly's hypothesis, especially if an MD is involved.
Another thing thing that could help you to 'sanitize' a bit the input PDB could be to 
pre-process the file with OpenBabel, with PDB as both input and output format. Sometimes 
this helps to fix atom name misalignments and/or exotic naming conventions.

Hope this helps,


On 11/18/2011 02:30 PM, Mihaly Mezei wrote:
> Hi,
> your molecule probably was distroted at a few places, so some bonds appear to be broke and that confuses ADT. Try a short minimization of the final structure and see it ADT likes it better.
> Mihaly Mezei
> Department of Structural and Chemical Biology, Mount Sinai School of Medicine
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  Stefano Forli, PhD

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