Dear Amber users,
I am simulating a glycosylated zinc metalloprotease with a Chloride ion in the active site. The main aim is to visualize large-scale hinging behaviour and interactions between the glycans.
Zn forcefield parameters were determined using the bonded approach in mcpb.py to coordinate the metal to his, his, glu and water. This behaved well during the minimization, heating and unrestrained equilibration and the chloride remained bound to an Arg. However, during the production md the chloride ion migrates towards the Zn and eventually displaces the coordinating water.
I would like to know how to apply a distance restraint between the Cl and Arg during production MD to prevent this from happening. Would it be considered an appropriate way to solve the problem?
Should a restraintmask be specified in the md.in<
http://md.in> file similar to positional restraints in minimization? If so, an example would be great since I can't find any online.
Kind regards
Lizelle Lubbe
PhD Chemical Biology (candidate)
University of Cape Town
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Received on Sat Jul 22 2017 - 11:00:02 PDT
