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.
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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Received on Fri Nov 28 2014 - 16:00:03 PST
