On Fri, Nov 28, 2014 at 6:45 PM, Jorgen Simonsen <jorgen589.gmail.com>
wrote:
> Hi all,
>
> I am trying to generate an octahedral complex with dummy atoms to mimic
> partial charges around the complex. As the complex is symmetric I have only
> added three atom types DD1-3.
>
I don't think atom types can have more than 2 letters in tleap, so I don't
think this will work. Try cutting them down to 2 letters (and still use
the frcmod file). One note, the dihedral section of the frcmod file should
be of the format:
XX-XX-XX-XX
where each field is 2 characters (one space if it's a 1-letter atom type).
In the snippet below, it looks like you have spaces in there.
HTH,
Jason
The problem is that I am not able to save the parameter or the topology
> file as tleap will not make them due to missing parameters:
>
> The first warning is this:
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-DD6-DD7-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-DD5-DD6-*
> +--- With Sp0 - Sp0
>
>
> I have not added a new atom type - maybe I should add one?
>
> The warnings continue with the following error message:
>
>
> Building proper torsion parameters.
> 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 5 6 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 5 7 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> and continues to give this warning/error
>
> ** No torsion terms for DZ3-ZN-DZ2-DZ4
> ** No torsion terms for DZ3-ZN-DZ3-DZ4
> ** No torsion terms for DZ3-ZN-DZ2-DZ4
> ** No torsion terms for DZ3-DZ2-ZN-DZ4
> ** No torsion terms for DZ3-DZ2-DZ3-DZ4
> ** No torsion terms for DZ3-DZ4-ZN-DZ4
> ** No torsion terms for DZ3-DZ4-DZ2-DZ4
> ** No torsion terms for DZ3-DZ4-DZ3-DZ4
> ** No torsion terms for DZ3-DZ4-DZ2-DZ4
> ** No torsion terms for DZ3-DZ2-ZN-DZ4
> ** No torsion terms for DZ3-DZ2-DZ3-DZ4
> ** No torsion terms for DZ2-ZN-DZ2-DZ3
> ** No torsion terms for DZ2-ZN-DZ2-DZ4
>
> and ends with the following message
>
> Building improper torsion parameters.
> total 0 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
>
> I have tried to add these to the frcmod-file
>
> DIHE
> X -DZ2 -DZ3 -DZ4 1 0.0 35.3 2.00
> X -ZN -DZ3 -DZ4 1 0.0 35.3 2.00
>
> IMPROPER
> X -ZN -DZ -X 0.0 180. 2.
> X -ZN -DZ -X 0.0 180. 2.
> X -ZN -DZ -X 0.0 180. 2.
> X -DZ -DZ -X 0.0 180. 2.
>
> but same amount of error mesages. I am using ambertools14 with the ff14SB
> force field - any recommendation how to fix this would be highly
> appreciated. Thanks
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 28 2014 - 16:00:03 PST
