Dear all,
When I using xleap to prepare my input parm, some error is happen. The
error message I have attached below, could you mind to help me?
Thank you for taking your time.
PS:I have correct the cys to cyx in the pdb file, which is formed the
disuflide bond. Using xleap to view the final structure, I found that these
disulfide bond are correctly to be recognized.
> saveamberparm ritu test.prmtop test.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Building proper torsion parameters.
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
total 1360 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 29 2010 - 23:00:03 PST
