I think you just misread the off file. The atom name is "MD" and the type
is "MM". Leap will hopefully build the dummy points correctly, but I
wouldn't expect the orientation to necessarily make too much sense. Try
changing the pdb line like this:
HETATM 2123 *MM* MD6 A 502 45.408 19.600 12.379 1.00 5.17
Mg
--->
HETATM 2123 *MD* MD6 A 502 45.408 19.600 12.379 1.00 5.17
Mg
I think that should work...
Brian
2012/1/16 Jesper Sørensen <jesorensen.ucsd.edu>
> Dear Tom,
>
> I am trying to use this post below of the MD6 magnesium parameters from
> your website.
> However, I am getting an error, because it seems Ambers ff10 doesn't know
> the atom type.
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-DX2-DZ1-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> ...
> ...
> ...
> Created a new atom named: MM within residue: .R<MD6 317>
> ERROR: Comparing atoms
> .R<MD6 317>.A<MD 1>,
> .R<MD6 317>.A<DY1 3>,
> .R<MD6 317>.A<DY2 4>, and
> .R<MD6 317>.A<DZ1 8>
> to atoms
> .R<MD6 317>.A<DZ2 9>,
> .R<MD6 317>.A<MD 1>,
> .R<MD6 317>.A<DY1 3>, and
> .R<MD6 317>.A<DY2 4>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named DZ2 from MD6 did not match !
> !
> !ABORTING.
>
> I have loaded the both files from your webiste
> loadamberParams MD6/frcmod.dummymg
> loadoff MD6/md6.off
>
> and in the PDB file I have renamed the original Magnesium ion to MD6
> (resname) and the atom to MM (atomtype for the center MD6 atom)
> HETATM 2123 MM MD6 A 502 45.408 19.600 12.379 1.00 5.17
> Mg
>
> Should I add atomtypes for each (dummy)atom in the MD6?
> For MM, I would given its geometry think the bond hybridization should be
> SP3D2, but AMBER doesn't allow that. So how should this be added?
>
> Any advise you could give me would be greatly appreciated.
>
> Kind regards,
> Jesper
> >
> >
> >
> >
> > -----
> > There is a point-charge model of Mg2+ in the AMBER force fields but
> > this is not a great approximation.
> >
> > I posted this before, but:
> >
> > In my simulations I have been using the Mg representation from:
> >
> > Oeschlaeger et al. Magnesium-cationic dummy atom molecules enhance
> > representation of DNA polymerase beta in molecular dynamics
> > simulations: improved accuracy in studies of structural features and
> > mutational effects. J Mol Biol. 2007 Feb 16;366(2):687-701. Epub 2006
> > Nov 3.
> >
> > I have prepared frcmod and off files, available at:
> >
> > http://atlas.physbio.mssm.edu/~tom/files/MD6.tar.gz
> >
> > You can use the leaprc.md6 in that archive with leap to load the
> parameters.
> >
> > Hope that helps,
> > --Tom
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
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Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Mon Jan 16 2012 - 20:30:02 PST
