On Tue, Jan 31, 2012, Vlastimil Zíma wrote:
> Hello Amberers,
>
> lately I work on simulations with calcium ions and I noticed it is quite
> complicated to use that ion in AMBER in comparison to other ions. There
> is atom type C0 defined for calcium ions in amber params e.g.:
>
> dat/leap/parm/parm99.dat:
> C0 40.08 calcium
>
> but the same atom type is used for carbon with hybridization sp2 e.g.:
>
> dat/leap/cmd/leaprc.ff99SB:
> addAtomTypes {
> { "C0" "C" "sp2" }
> }
Looks like a typo to me: should be { "C0" "Ca" "sp3" }. I don't see any
place that atom type C0 is used other than as calcium. [Others on the
list can correct me if needed.] Note that, as with magnesium, you should
be cautious about using simple fixed charge models for divalent ions.
....dac
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Received on Tue Jan 31 2012 - 07:00:04 PST
