[AMBER] crystallographic artifacts

From: ashwini gupta <wini657.gmail.com>
Date: Tue, 10 Apr 2012 12:03:54 +0530

Dear AmberUsers,

I am doing a metalloprotein simulation with three metal sites. Two of the
metal sites are known to be a part of the protein but the significance of
third metal site is not described and some suggest that it could be a
crystallographic artifact. Another reason for this is that the third metal
sites are liganded to three water molecule and two histidine.

For the first two metal site I have performed MCPB, which is a bonded
approach for metal parameterization. However, for the third metal site I
dont want to go for the bonded approach as if i do so I might bias the
third metal site to be a part of the protein and also i will fix the water
molecule. Another approach could be to not parameterize the Fe ion and keep
it in the system as an ion and neutralise the system using Cl ion. Fix the
ligand and ions for the first 100 ps or so and then let the system to
simulate and see whether its a part of the protein for the complete
simulation or for just some parts of the simulation.

Can anyone give me a few suggestions and advice regarding the following.

Thanks & Regards

AMBER mailing list
Received on Tue Apr 10 2012 - 00:00:03 PDT
Custom Search