Hello,
I am computing free energy of binding for few neuraminidase inhibitors.
Now, there is Ca2+ atom in the protein (Problably Dr. Ross Walker would
know better since he published one paper on this <Nature
Communications 2, Article
number: 388 doi:10.1038/ncomms1390>). For Ca2+ atoms I took the parameters
reported by G. Bradbrook (
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/ion/metals_inf.html
) Now, the atom name for calcium here is "KA" to avoid using "CA" which
correspondence to sp2 aromatic carbon in 6-membered ring with 1
substituent. However, I had no problems running MD but when I open one of
the out files while running MM-PBSA, I read the following message "Using
carbon SA parms for atom typeKA" I have attached one of the out files
along with this E-mail, and this message can be found on line 111.
Please help me understand how serious is this warning.
Many Thanks in advance.
*Elvis Martis* PhD Student, Bombay College of Pharmacy
[image: photo] Website: http://www.elvismartis.in
<
http://www.elvismartis.in/>
Address: Kalina, Santa Cruz [E]
<
https://in.linkedin.com/in/elvisadrianmartis>
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Received on Tue Apr 19 2016 - 22:00:03 PDT
