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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Received on Mon Jan 16 2012 - 19:00:03 PST
