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 [Aside: the ff99SB force field is way out of date.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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 28 2019 - 04:30:01 PST
