AMBER Archive (2007)

Subject: AMBER: Using TLEAP to set up MD in the crystal lattice space?

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Mon Aug 13 2007 - 16:09:51 CDT

Hello,

    I would like to do an MD simulation in the crystal lattice space. The
protein crystal is orthorhombic (space group I222), and I have made a PDB
file containing the protein's symmetry-related neighbors in its unit cell.

    What would be the best way to obtain the topology and starting
coordinate files to do this simulation in the crystal lattice? Please
note that although I have reconstructed the crystal unit cell, come
portions of some of the symmetric units will hang out one side of the
original unit cells and into neighboring cells. I'm also not sure exactly
how to solvate this system, but I think the best strategy would be to hold
the protein with tight restraints for successive additions of water
molecules and simulation in the NVT ensemble, then simulation in the NPT
ensemble while maintaining the protein atom restraints as small numbers of
water molecules are added or taken away until the pressure stabilizes at
1atm with the right unit cell volume.

Thanks for any suggestions!

Dave
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