Dear Dr. Case,
The main issue is, the metals start to move away from each other. The initial distance between the two magnesium atoms is 3.5 A. By 1 ns the distance is 6 A. Also, there are three oxygens of ligand coordinating to the two magnesium in the crystal structure, in addition to binding site residues coordinating the magnesium ions. This coordination geometry that is required for bimetal chelation is disturbed and the key interactions oxygens in ligand started to move away from the metal.
I tried MG2 this time in desc
> desc MG2.1
RESIDUE name: MG2
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 0
Type: undefined
Connection atoms:
Improper torsions:
Contents:
A<MG 1>
Where am I going wrong?
The command to load force field is: - bsub -P Pan -app amber12-ib -Is -q interactive tleap -f leaprc.ff99SB
I am using the following version to submit jobs in cluster: module load amber/12/openmpi-1.6.0-intel
Thanks and regards,
Latha.
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Received on Mon Aug 12 2013 - 09:00:03 PDT
