Hey, AMBER users,
I built a solvent box of chloroform with tleap. When I visualized the pdb
file with VMD, it is found that the bond lengths of C-Cl even in the same
molecule are different (1.72-1.83 angstrom, I just cheked three molecules),
which will cause the C-Cl bond to be cleaved during the MD calculation. I do
not think tt is reasonable. Is there anyone who ever encountered this
problem? What's wrong with my solvent box?
Any help will be hghly appreciated.
Happy New Year!
WJ
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Received on Mon Jan 05 2009 - 01:12:06 PST
