Hi All,
An update to my post...
In the beginning of my leap log there is some errors with the addAtomTypes... This could explain why magnesium is having some problems. I am using "default" settings, so is this a bug in the code/parameter files then?
source /Users/jsx/Apps/amber11/dat/leap/cmd/leaprc.ff10
----- Source: /Users/jsx/Apps/amber11/dat/leap/cmd/leaprc.ff10
----- Source of /Users/jsx/Apps/amber11/dat/leap/cmd/leaprc.ff10 done
Log file: ./leap.log
addAtomTypes: type Cl- - max length is 2
addAtomTypes: type Br- - max length is 2
addAtomTypes: type Li+ - max length is 2
addAtomTypes: type Na+ - max length is 2
addAtomTypes: type Rb+ - max length is 2
addAtomTypes: type Cs+ - max length is 2
addAtomTypes: type Mg+ - max length is 2
Loading parameters: /Users/jsx/Apps/amber11/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/amino10.lib
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/aminoct10.lib
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/aminont10.lib
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/nucleic10.lib
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/ions08.lib
Loading library: /Users/jsx/Apps/amber11/dat/leap/lib/solvents.lib
Best,
Jesper
On Jan 18, 2012, at 8:05 AM, Jesper Sørensen wrote:
> Hi All,
>
> 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+
>
> If I rename the atom or residue name to any of the following, MG, MG2 etc.
> leap does either not recognize the unit, or it adds a missing heavy atom.
>
> In the top of my tleap script I am sourcing these files
> source leaprc.ff10
> loadAmberParams frcmod.tip4pew
> loadAmberParams frcmod.ionsjc_tip4pew
>
> Any suggestions?
>
> Best regards,
> Jesper
>
>
>
>
> ---
> Jesper Sørensen, Ph.D.
> Postdoctoral Researcher, Amarolab
> Department of Chemistry and Biochemistry
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093-0365
> http://amarolab.ucsd.edu
>
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Received on Wed Jan 18 2012 - 09:00:02 PST
