AMBER Archive (2005)

Subject: AMBER: MM_PBSA for NMR restrained structures

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri May 20 2005 - 03:36:10 CDT

Dear Amber community,

I have a question about PB/SA (invoked by the MM_PBSA)

computations for NMR restrained structures.

Finite-difference PB/SA computations depend on the
configuration of a solute as described by
Q. Lu & R. Luo (2003). J. Chem. Phys. 119,
11035-11047.

I have an NMR restrained ligand molecule. Only the
final snapshot of trajectory
possesses the lowest RMS deviation from the NMR data.
Is it necessary to run the MM_PBSA
for multiple snapshots of the trajectory, or just a
PB/SA computation for the last snapshot would
suffice ?
If running MM_PBSA for multiple snapshots is that
necessary, would it be a good idea to run
an extended MD by restraining the final NMR Cartesian
coordinates to itself and use the new trajectory
for MM_PBSA computations?

Any plausible strategy that you can comment on this
will be greatly appreciated.

regards,

jenk.
      

                
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