Dear Amber Users,
I am trying to use tleap to generate crd and top files for "Bisphenol A diglycidyl ether" containing di-epoxide rings.
When I used tleap with this structure, there are lots of errors as shown below.
(mol2 file was generated from antechamber.)
I believe that this structure is very general to be used for simulations. However, gaff force field does not produce correct parameters.
Therefore, I used parmchk to find missing paramters and it suggested some parameters with high penalty score 92.0, 179.0, and 266.0.
As I said, I think that the ring strcuture is not unique in chemisty and does anyone know why gaff does not find parameters for it?
Thanks.
Chang
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 1 9 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 1 7 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 4 11 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 4 8 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 7 9 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Note.
1-4: angle 8 11 duplicates bond ('triangular' bond) or angle ('square' bond)
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-op-cx-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-op-cx-c3
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-op-cx
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-op-cx
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-op-cx-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-op-cx-c3
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for cx-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-op-cx
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-op-cx
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for op-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-os
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-h1
/home/Hy/Packages/amber18/bin/teLeap: Error!
** No torsion terms for h1-cx-c3-h1
Building improper torsion parameters.
total 10 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/home/Hy/Packages/amber18/bin/teLeap: Warning!
Parameter file was not saved.
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Received on Mon Dec 17 2018 - 15:30:02 PST
