So is this the one you recommend frcmod.ionslrcm_iod? Or one with the TIP3P?
Thanks
On Mon, Oct 20, 2014 at 1:38 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Chinthaka,
>
> You can use that set for the bonded model. Since it is specified for
> 12-6-4 model, it would be
> *better* for you to use the parameter sets specified for 12-6 model. The
> related information is in
> the page 44 and 45 at Amber 14 manual.
> http://ambermd.org/doc12/Amber14.pdf
>
> You can check the related paper here:
> http://pubs.acs.org/doi/abs/10.1021/ct400146w
>
> My suggestion is using the CM or IOD parameter set for the VDW parameters
> in the bonded model.
>
> HTH,
> Pengfei
>
> On Oct 20, 2014, at 2:28 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>
> wrote:
>
> > 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
> >>> _______________________________________________
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> >>>
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> >>
> >
> >
> >
> > --
> > Chinthaka Nadun Ratnaweera
> > Hand Lab Rm 1126
> > Department of Chemistry
> > Box 9573
> > Mississippi State University
> > Mississippi State, MS 39762-9573
> > _______________________________________________
> > 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 - 12:00:02 PDT
