[gmx-users] conformational change

[Chris Shaw]

Hi all, 

I have a ligand for which I have written 2 topologies and inactive conformation & an active conformation. I relax the inactive structure and all is OK. When I then use the final relaxed inactive conformation as the input for the conformational change the ligand stays in the inactive conformation. I have tried increasing the parameters in my topology files for angles, dihedrals incase there was a high transition state, but still nothing. Can anyone help, are distance restraints in the top file an option to try to coax the inactive to the active structures.

Cheers

Chris




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