NBFIX parameters for Calcium ion

From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Thu Jun 09 2016 - 04:49:04 CDT

Dear NAMD users,

I have a question regarding the ions and NBFIX parameters in charmm force
field. In the charmm force field parameter file there are NBFIXes only for
K and Na ions with Cl, and between Na and carboxylate. I wished to know
when considering Ca ion and its interaction with a protein, what should be
done? Is it possible to add it to the force filed file? And if so, how?

As far as I can see from the file, in the NBFIX part, sigma parameter is
approximately close to the average of sigmas for Cl and Na. On the other
hand, the epsilon of Na and Ca without NBFIXes are very close. So is it
possible to consider a NBFIX parameter for Ca like this: the average of
sigmas for sigma and the same epsilon as the one for Na and then add it to
the file?
What about the NBFIX between carboxylate and Calcium?

Your help would be greatly appreciated.

Best regards,

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