On Thu, 2015-07-09 at 20:27 -0600, Ahmed Ayoub wrote:
> Dear Amber users,
>
> I'm using MMGBSA with a system that has a magnesium ion. I keep getting
> this message in the intermediate output files "_MMPBSA_complex.mdcrd.0 for
> example":
>
> "Using carbon SA parms for atom type MG"
>
> is that normal?
Yes. Ion parameters have not been optimized for implicit solvent models
since ions are typically modeled as part of the solvent environment
through a Debye-like screening term. Any atoms that are not recognized
by sander are given "default" surface area and intrinsic solvation radii
that are equivalent to those of carbon. Hence the message.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 10 2015 - 05:00:03 PDT
