Hi,
If your magnesium has no bond, only parameters you can change are LJ
parameters and charge of the ion.
If you want to adjust LJ parameters, you should prepare frcmod file and put
the numbers below NONB section. Default atom type for magnesium ion is 'MG'
in ff99-series. If you want to change the charge, use 'set' command in
leap. Default residue name is MG2. So, if your initial model is from a pdb
file, rename the residue name with MG2 for the magnesium ion.
However, you should be aware that current model of MG (in ff99-series) may
not represent your model correctly.
2010/10/20 Andrew Voronkov <drugdesign.yandex.ru>
> If I just load 99SB and GAFF and then .frcmod and .lib files for the small
> molecule then when I am trying to save .prmtop and .inpcrd files I get the
> next error>
> > saveamberparm rab rab.prmtop rab.inpcrd
> Checking Unit.
> FATAL: Atom .R<MGA 172>.A<MG 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> >
>
> so I am curious if I should make .frcmod file and .lib files for magnesium
> ion or not.
> If I should that which non/bonded parameters I should use? (below is
> .frcmod file which I've used for zinc)
>
>
> Zinc 2+ Params
> MASS
> ZN 65.38
>
> BOND
>
> ANGL
>
> DIHE
>
> NONB
> ZN 1.85 0.06
>
>
> 20.10.10, 17:36, "Dmitry Nilov" <nilovdm.gmail.com>:
>
> > You should use both protein (for example ff99SB, describing protein
> > and MG) and gaff (describing ligand) force fields simultaneously:
> >
> > tleap -s -f leaprc.ff99SB
> > > source leaprc.gaff
> > > loadamberparams ligand.frcmod
> > > loadoff ligand.lib
> > > mol = loadpdb protein.pdb
> > > saveamberparm mol protein.prmtop protein.inpcrd
> >
> >
> >
> > On Tue, Oct 19, 2010 at 6:12 PM, Andrew Voronkov wrote:
> > > Dear Amber users,
> > > I have a biotarget which has magnesium ion together with the small
> molecule in the binding site. I have made parametrization in GAFF with
> antechamber for the ligand, but then I've gota problem with magnesium ion.
> I actually was sure that it is included in the Amber force fields as Na+
> ions and I can't find much information in manuals about this. Should I
> include magnesium ion in the protein or in small ligand or make a separate
> library for it? Should I use gaff or protein force field?
> > >
> > >> saveamberparm rab 1z2ang_w.prmtop 1z2ang_w.inpcrd
> > > Checking Unit.
> > > FATAL: Atom .R.A does not have a type.
> > > Failed to generate parameters
> > > Parameter file was not saved.
> > >
> > > Sincerely yours,
> > > Andrew
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
>
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>
--
Best,
InSuk Joung
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Received on Wed Oct 20 2010 - 10:30:06 PDT
