You could a) change the force field used b) increase the docking resolution c) switch to a different program e.g. FRED from OpenEye d) examine if you limited the amount of generated confirmers for your ligand. If you have two or three rotatable bonds you can easily generate >1000. And it seems your molecule might have more than that e) maybe you can model the ionic strength of the crystallization conditions (not sure schroedinger has a function for that) f) reach out to the folks at Schroedinger to help you.
Some thoughts, Jürgen __________________________________________ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Jan 3, 2024, at 18:23, Thripthi Shenoy <thripthishe...@gmail.com> wrote: Greetings to all. I am trying to dock a co crystallized ligand using GLIDE. The co crystallized ligand is a big molecule with multiple rotatable bonds. GLIDE is unable to regenerate the ligand pose. I tried limiting the rotatable bonds, but in vain. I would be grateful to receive any advice or suggestion as to how I can proceed. Thanking you in advance, Regards, Thripthi S. ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
