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 šproblem 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: šAtom .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
> >
>
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 20 2010 - 09:30:06 PDT
