Hi,
It seems like you're using the LCPO surface area model (gbsa=1). I
don't think there are LCPO parameters for calcium anyway, so no matter
what it would get assigned carbon parameters by default.
That said, my personal opinion is that the LCPO model is so
approximate anyway that errors in the model itself will be larger than
errors from assigning carbon SA parameters to your single calcium.
-Dan
On Tue, Apr 19, 2016 at 10:56 PM, Elvis Martis <elvis.martis.bcp.edu.in> wrote:
> 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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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Apr 21 2016 - 10:30:05 PDT
