Article ID: 752 - Last Modified: May 16, 2011
I have been docking a compound with a bond from iodine to an aromatic carbon. The bond length in my minimized input structure is 2.08 Å (matching the crystal value of 2.14 Å), but the output file from Glide had a bond length of 1.55 Å. What's going on?
The C-I bond is shortening because the version of Glide you are running is using the OPLS_2001 force field by default, which does not have dedicated parameters for iodine bonding. Default bond-stretch parameters are used, with an equilibrium distance of 1.529 Å. OPLS_2005 has greatly improved coverage of such compounds, and will yield a minimized aromatic C-I bond length of 2.091 Å. OPLS_2005 was made the default force field for docking in Suite 2011.
Two options to address this problem in earlier releases are:
1) Turn off post-docking minimization, so that the input bond lengths and bond angles are preserved, and
2) Use OPLS_2005 instead of OPLS_2001 for docking, which you can do by setting the environment variable SCHRODINGER_MMIM_GLIDE_FF to OPLS_2005 prior to starting your Maestro session, or adding the line
to the jobname.in file, and running the job from the command line with
Keywords: iodine, carbon-iodine bond, bond-stretch parameters, OPLS_2001, OPLS_2005, Glide, Maestro
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