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?
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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Received on Wed Jan 18 2012 - 09:30:02 PST
