We previously followed
http://archive.ambermd.org/200709/0211.html to make
a library file. Still this is a nonbonded model. However in long run
Calcium's were not stable. Can you please send the details or a link to
create bonded parameters.
On Mon, Oct 20, 2014 at 1:50 PM, Ken Merz <kmerz1.gmail.com> wrote:
> Hi,
> You could use the parameter sets mentioned by Pengfei, but you might want
> to try the nonbonded model first. It might work fine without needing to
> create the bonded parameters, etc. Worth a quick test. Kennie
>
> > On Oct 20, 2014, at 2:47 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>
> wrote:
> >
> > 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
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
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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
> >>
> >> _______________________________________________
> >> AMBER mailing list
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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 - 12:30:02 PDT
