[gmx-users] Ligand moving during MD course.

Raju rajiv at kaist.ac.kr
Wed Jul 30 10:44:59 CEST 2014

Dear gmx users,

I have simulated the crystal structure prion with its inhibitor using charmm27.ff force field by obtaining the inhibitor parameters from http://www.swissparam.ch/.

After i ran the production for 10 ns, the output shows the inhibitor moving ~ 3 Angstrom from the cavity and contacting close to the cavity the few more different residues from protein. Even i could see the inhibitor moving in equilibrium state  (NPT). Moreover, i have not used any constrains for inhibitor. 

I have also tried another prion crystal structure with its different inhibitor as well docked inhibitors but in all results, the inhibitors were moving in different direction within 10 ns for MD production. 

I just worried whether i am using any wrong protocol or naturally it does happen for specific proteins? 

Your suggestion would be greatly appreciated. Thanks.


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