On Mon, Apr 13, 2015 at 7:25 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Apr 12, 2015, Carlos Romero wrote:
> >
> > Thanks a lot for your help. I tried to use default ions, but when i
> tried
> > to save prmtop and inpcrd file, I got a message that said:
> >
> > For atom: .R<CO 405>.A<CO 1> Could not find vdW (or other) parameters for
> > type: Co2+
>
> For calcium, I guess you should copy the parameters in parm99.dat into your
> frcmod file, and load that. You could also do a literature search to see
> what
> parameters other are using. Maybe someone with calcium experience on the
> list
> can respond.
>
> [Pengfei: why are there "lsm" parameters for +1, +3 and +4 ions, but not
> +2?]
>
There are, they are just named differently. The +2 ions were the original
work (frcmod.ionslrcm_cm_{tip3p,spce,tip4pew}), so the author list is
slightly different (ergo, slightly different names). Also, I think the lsm
parameters are only part of the developer tree (I think they were added in
the last year).
So to Carlos -- make sure you source the frcmod.ionslrcm_cm_tip3p
parameters (or the one for spce or tip4pew if you use either of those water
models).
I would suggest against copying the parameters from parm99.dat, since these
new ones should give better behavior.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 13 2015 - 07:00:05 PDT
