My case is simple. I am trying to simulate Ca2+ coordinated to protein.
Thank you.
On Sat, Mar 2, 2019 at 1:13 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Note that if you're trying to simulate a covalently bound calcium, you
> may want to generate parameters using MCPB.py since it's not clear the
> calcium ion parameters are transferable to a bound calcium.
>
> -Dan
>
> On Thu, Feb 28, 2019 at 7:24 AM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
> >
> > Dear David,
> >
> > I could generate topology and coordinate for Ca2+ bound protein with
> amber
> > 18, simply by sourcing "source leaprc.water.tip3p".
> > I could not find "desc" command in the "bin" folder. I wanted to verify
> the
> > presence of calcium ions.
> >
> > This is how my tleap file looks.
> > -----------------
> > source leaprc.ff99SB
> > source leaprc.water.tip3p
> > set default PBradii mbondi2
> > m = loadpdb AH_noH.pdb
> > saveamberparm m AH_noH.prmtop AH_noH.inpcrd
> > quit
> > ----------------
> > I will do REMD using Generalized Born (GB-OBC; igb=5) solvent model as it
> > is for comparison purpose.
> > Is it ok to simulate ion bound protein using GB-OBC model?
> >
> > Thank you so much for your help.
> >
> > With best regards,
> > Sunita
> >
> > On Tue, Feb 12, 2019 at 7:56 PM David Case <david.case.rutgers.edu>
> wrote:
> >
> > > On Tue, Feb 12, 2019, Sunita Patel wrote:
> > >
> > > >Can you please provide some links. I was thinking it would be straight
> > > >forward like protein atom types.
> > >
> > > It *is* straightforward, although I agree that the manual section on
> > > ions is more complex than it needs to be. Once you select a water
> model
> > > (via "source leaprc.water.xxxx"), monoatomic ions for that model are
> > > automatically loaded as well. The exact parameters used are printed to
> > > the screen when you load a water file.
> > >
> > > You can use the "desc" command in tleap to see which ions are present.
> > > Following the PDB standard, the residue and atom name for calcium2+ are
> > > both "CA". So make sure your input PDB file labels calcium as CA, and
> you
> > > should be fine.
> > >
> > > [Aside: the ff99SB force field is way out of date. If you are not
> using
> > > AmberTools18, you should upgrade to that version, and use ff14SB for
> > > proteins.]
> > >
> > > [Aside to developers: the "Ions" section of the Reference Manual is
> > > written only for some hypothetical super-expert who wants to know
> > > details of ion parameters we no longer use. Can someone add an opening
> > > paragraph describing what users are actually supposed to do in
> practice,
> > > i.e. that the water leaprc files include ions, and that the recommended
> > > parameters are indentified there?]
> > >
> > > ...good luck....dac
> > >
> > >
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> > >
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Received on Sat Mar 02 2019 - 00:00:01 PST
