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 [Aside: the ff99SB force field is way out of date.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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Mar 01 2019 - 07:30:03 PST
