Dear amber users,
I am trying to save parm and top file in leap but I am getting error with
disulfid bonds repeatedly. I have renamed bonded cys to cyx and I have
checked the bond commands. Please let me know what is the problem. I can
send you the pdb if needed.
error:
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - S
Building angle parameters.
Could not find angle parameter: HS - SH - S
Could not find angle parameter: SH - S - CT
Could not find angle parameter: CT - SH - S
Building proper torsion parameters.
** No torsion terms for HS-SH-S-CT
** No torsion terms for CT-SH-S-CT
Building improper torsion parameters.
total 3190 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
leap bond commands:
bond gp0.7.SG gp0.34.SG
bond gp0.133.SG gp0.163.SG
bond gp0.166.SG gp0.175.SG
bond gp0.170.SG gp0.183.SG
bond gp0.191.SG gp0.199.SG
bond gp0.195.SG gp0.207.SG
bond gp0.208.SG gp0.216.SG
bond gp0.212.SG gp0.224.SG
bond gp0.227.SG gp0.236.SG
bond gp0.240.SG gp0.267.SG
bond gp0.271.SG gp0.283.SG
bond gp0.287.SG gp0.302.SG
bond gp0.305.SG gp0.309.SG
bond gp0.313.SG gp0.338.SG
bond gp0.446.SG gp0.475.SG
bond gp0.482.SG gp0.491.SG
bond gp0.486.SG gp0.499.SG
bond gp0.502.SG gp0.511.SG
bond gp0.515.SG gp0.531.SG
bond gp0.534.SG gp0.547.SG
bond gp0.538.SG gp0.555.SG
bond gp0.558.SG gp0.567.SG
bond gp0.571.SG gp0.593.SG
bond gp0.596.SG gp0.604.SG
bond gp0.600.SG gp0.612.SG
bond gp0.616.SG gp0.630.SG
bond gp0.624.SG gp0.641.SG
bond gp0.643.SG gp0.652.SG
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Received on Mon Feb 22 2016 - 01:30:03 PST
