[Dock-fans] how to convert mol2 format to sdf format?

Andrew Harris Wiser awiser at ucsc.edu
Fri Jul 11 12:34:24 PDT 2008

Hi Yolanda,

One of the issues I ran into when converting Dock results 
from mol2 to sdf was extracting the scores from the 
comment fields for each compound.  I tried performing 
conversions in both openbabel and Pipeline Pilot, but in 
both cases the comment fields were lost making analysis of 
the results outside of ViewDock tedious.  I ended up 
writing a short perl script to extract the comment fields 
into a tab delimited file that can be easily merged in 
Pipeline Pilot.  While this is an extra step in converting 
formats, the end result, an sdf file where each compound 
has properties reflecting the results from Dock, is very 

This is something I thought you might want to consider in 
addition to the actual conversion process since some of 
the data gets lost in translation.  I tested the website 
provided and it too seemed to have this problem.

As a side note is there a way to output the scores from 
Dock into fields that do not require this extra step?  I'm 
still learning Dock, but I didn't see an option to change 
this.  Based on the mol2 format specifications it seemed 
like mol2 files do not have the freedom of sdf/sd/mol 
files with property fields.

-Andrew Wiser

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