Hi Brian,
Thanks for the answer, but it didn't work. I still get the same error.
Best,
Jesper
On Jan 16, 2012, at 8:08 PM, Brian Radak wrote:
> 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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>>
>
>
>
> --
> ================================ 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
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> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
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Received on Mon Jan 16 2012 - 22:00:02 PST
