Dear list,
I am trying to simulate protein unfolding on hydroxyapatite surface using AMBER MD package. I got the parameters for HAP (based on the interface force field). I prepared the system where the protein was placed 7 A away from the HAP surface. Water was later added to the system, I am trying to hold the HAP surface rigid by applying position restraints but the surface deforms immediately during minimisation. This problem is also documented in the mailing list.
Any suggestion running simulation of HAP in AMBER MD package would be helpful.
http://archive.ambermd.org/201008/0070.html
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