AMBER Archive (2009)

Subject: AMBER: CHCl3 solvent box

From: WJ Ding (
Date: Sun Jan 04 2009 - 16:24:48 CST

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!


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