Dear Amber Users,
I am simulating an enzyme with Zn-CCCC tetrahedral coordination being present at
the active site. I used the ZAFF parameters for Zn-CCCC. However, when I do
saveamberparm, the following warning appears in the log file:
unperturbed charge of the unit: 0.231630 is not zero.
I am using addions (Cl-) to neutralize 1 unit of charge, leaving the
non-integral unit behind. How can I neutralize a non-integral charge. If I
ignore this warning and go ahead with the files for MD, will that eventually
lead to a problem.
Any help/suggestions regarding this will be highly appreciated.
Thanks a lot in advance.
Best Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore-560012
India
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Received on Fri Jul 22 2011 - 06:00:05 PDT
