2012/1/18 Jesper Sørensen <jesorensen.ucsd.edu>
> I thought I had tried that solution already, but now it works. Thanks
> Prof. Case.
>
> Is this not a bug still though? Not that I mind changing the source
> code/parameter files at all, but shouldn't this work automatically.
> If it is the naming in the PDB file that is the problem, then that would
> be an easier fix for users.
>
> Also, I am a little curious by the line in the Log file: ./leap.log
> addAtomTypes: type Mg+ - max length is 2
>
> Does this have something to do with the a naming of ions?
>
Yes. Ions never used to be labeled with their charge (sign) before. Now
that they are, there are atom names that have 3 characters where there
weren't any before. The next leap in AmberTools Next should not have this
warning anymore.
All the best,
Jason
>
> Best regards,
> Jesper
>
>
> On Jan 18, 2012, at 8:49 AM, David A Case wrote:
>
> > On Wed, Jan 18, 2012, Jesper Sørensen wrote:
> >>
> >> I am trying to create my system using tleap, but I am an errors
> >> regarding a magnesium ion.
> >>
> >> When in the PDB file it is called
> >> HETATM 2123 Mg+ Mg+ A 502 45.408 19.600 12.379 1.00 5.17
> MG
> >>
> >> tleap recognizes it correctly, but when it comes time to output a prmtop
> >> and crd file it says it does not have parameters for this.
> >> For atom: .R<Mg+ 317>.A<Mg+ 1> Could not find type: Mg+
> >
> > Please see http://archive.ambermd.org/201111/0020.html. (You can find
> this
> > by searching on "magnesium mg+" at the archive of the Amber mailing
> list.)
> >
> > ...dac
> >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 18 2012 - 11:00:03 PST
