Hi,
I am having trouble with Magnesium charges. It seems the charge of Magnesium is considered as zero and the two magnesium ions start to move away from each other starting from minimization to production. The bimetal chelation with ligand is important for my study. Hence, I cannot impose constraints or restraints on metal ions.
I am using the following commands:
bsub -P Pan -app amber12-ib -Is -q interactive tleap -f leaprc.ff99SB
Source leaprc.ff99SB
receptor = loadpdb receptor.pdb
charge receptor
My pdb reads as follows:
ATOM 1823 MG MG2 303 9.624 20.257 -6.444 1.00 59.85 MG2+
ATOM 1824 MG MG2 304 7.883 17.577 -8.538 1.00110.66 MG2+
Any help/suggestion in this regard is appreciated.
Thanks and regards,
Latha.
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Received on Thu Aug 08 2013 - 14:30:02 PDT
