Thank you very much!
It works!
Best regards,
Andrew
20.10.10, 21:11, "Dmitry Nilov" <nilovdm.gmail.com>:
> Try to rename MGA into MG2
>
> 2010/10/20 Andrew Voronkov :
> > If I just load š99SB 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: šAtom .R.A 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 šnon/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" :
> >
> >> You should use both protein (for example ff99SB, describing protein
> >> šand MG) and gaff (describing ligand) force fields simultaneously:
> >>
> >> štleap -s -f leaprc.ff99SB
> >> š> source leaprc.gaff
> >> š> loadamberparams ligand.frcmod
> >> š> loadoff ligand.lib
> >> š> mol = loadpdb protein.pdb
> >> š> saveamberparm mol protein.prmtop protein.inpcrd
> >>
> >>
> >>
> >> šOn Tue, Oct 19, 2010 at 6:12 PM, Andrew Voronkov šwrote:
> >> š> Dear Amber users,
> >> š> 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?
> >> š>
> >> š>> saveamberparm rab 1z2ang_w.prmtop 1z2ang_w.inpcrd
> >> š> Checking Unit.
> >> š> FATAL: šAtom .R.A does not have a type.
> >> š> Failed to generate parameters
> >> š> Parameter file was not saved.
> >> š>
> >> š> Sincerely yours,
> >> š> Andrew
> >> š>
> >> š> _______________________________________________
> >> š> AMBER mailing list
> >> š> AMBER.ambermd.org
> >> š> http://lists.ambermd.org/mailman/listinfo/amber
> >> š>
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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Received on Thu Oct 21 2010 - 00:30:05 PDT
