Ca parameters are there in the frcmod.ionslm_1264_tip3p in amber14
developed by Li/Merz for TIP3P water (12-6-4 set).
Can someone comment that this parameters are OK to use for bound Ca inside
a protein?
On Mon, Oct 20, 2014 at 12:57 PM, jinfeng liu <jinfengliu1119.gmail.com>
wrote:
> It is a free ion. Ok, I have read the amber manual for that. Thank you all.
>
> 2014-10-20 10:44 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
>
> > On Mon, Oct 20, 2014 at 12:35 PM, jinfeng liu <jinfengliu1119.gmail.com>
> > wrote:
> >
> > > Dear Amber users,
> > >
> > > I want to run MD simulation for a protein which contains a calcium. I
> > know
> > > the parameters of calcium are included in amber. So, what should I do
> to
> > > get amber know the calcium in the pdb. Thank you.
> > >
> >
> > Please describe better what you are trying to do. Is it a bound
> calcium?
> > Do you want to model it using covalent bonds to various residues in your
> > protein? Do you just want it as a free ion (if so, see chapter 3 section
> > 9)? What have you tried so far? Did it not work? How did it fail?
> >
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Department of Chemistry
Box 9573
Mississippi State University
Mississippi State, MS 39762-9573
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Received on Mon Oct 20 2014 - 11:30:02 PDT
