[gmx-users] Huge conformational change of ATP molecules

Zheng Ruan zruan1991 at gmail.com
Tue Feb 23 06:18:06 CET 2016

Hi Gromacs Users,

I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
amber99sb-ildn force field with parameters of ATP derived from the database
of Richard Bryce.

What surprised me is that the ATP molecules displays a huge flexibility and
conformational change. First, it slipped out from the starting binding
pocket. In addition, the plane of adenine ring and ribose sugar rotate to
about 180 degree after 10ns, making the ATP molecule looks weird. I never
run a MD of a protein with ligand before. Is this something normal? What
are possible causes for this? Maybe I should try some other ATP protein
complex to see if the same thing happens? Thank you!


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