Hi all
I have been trying to run amber with a peptide conjugated with unsual ADP-ribose attachment and keep getting this error whatever I try. Any suggestions?
> saveamberparm 15aa_APR 15aa_APR.prmtop 15aa_APR.inpcrd
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.097100 is not integral.
WARNING: The unperturbed charge of the unit: 0.097100 is not zero.
ERROR: The perturbed charge: 0.097100 is not integral.
WARNING: The perturbed charge: 0.097100 is not zero.
-- ignoring the errors and warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: O2 - C3
Could not find bond parameter for: CD - NA
Could not find bond parameter for: CD - H5
Could not find bond parameter for: NC - CD
Could not find bond parameter for: NH - HN
Could not find bond parameter for: NH - HN
Could not find bond parameter for: CA - NH
Could not find bond parameter for: C3 - OS
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - OS
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: NB - CA
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - OH
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - OH
Could not find bond parameter for: CA - H5
Could not find bond parameter for: CA - NB
Could not find bond parameter for: NB - CA
Could not find bond parameter for: NB - CA
Could not find bond parameter for: C3 - OS
Could not find bond parameter for: C3 - OH
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - H2
Could not find bond parameter for: C3 - NA
Could not find bond parameter for: C3 - H2
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - OH
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: OS - C3
Could not find bond parameter for: C3 - OS
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - C3
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: C3 - OS
Could not find bond parameter for: C3 - H1
Could not find bond parameter for: P5 - O
Could not find bond parameter for: P5 - O
Could not find bond parameter for: P5 - O
Could not find bond parameter for: P5 - O
Building angle parameters.
Could not find angle parameter: O2 - C3 - C3
Could not find angle parameter: O2 - C3 - H1
Could not find angle parameter: C - O2 - C3
Could not find angle parameter: H1 - C3 - H1
Could not find angle parameter: H1 - C3 - H1
Could not find angle parameter: HN - NH - HN
Could not find angle parameter: NA - CD - H5
Could not find angle parameter: NA - C3 - H2
Could not find angle parameter: NC - CD - NA
Could not find angle parameter: NC - CD - H5
Could not find angle parameter: CA - NH - HN
Could not find angle parameter: CA - NH - HN
Could not find angle parameter: CA - CA - NC
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: CA - CA - NH
Could not find angle parameter: CA - NC - CD
Could not find angle parameter: CA - CA - NA
Could not find angle parameter: OS - C3 - C3
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: OS - C3 - H2
Could not find angle parameter: C3 - C3 - OS
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: CA - CA - NC
Could not find angle parameter: CA - NA - CD
Could not find angle parameter: OH - C3 - C3
Could not find angle parameter: OH - C3 - H1
Could not find angle parameter: NB - CA - CA
Could not find angle parameter: NB - CA - NA
Could not find angle parameter: NB - CA - H5
Could not find angle parameter: C3 - C3 - C3
Could not find angle parameter: C3 - C3 - OS
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - OH - HO
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: OH - C3 - C3
Could not find angle parameter: OH - C3 - H1
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: C3 - C3 - C3
Could not find angle parameter: C3 - C3 - OH
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - OH - HO
Could not find angle parameter: C3 - C3 - OS
Could not find angle parameter: C3 - C3 - H2
Could not find angle parameter: CA - NB - CA
Could not find angle parameter: CA - NB - CA
Could not find angle parameter: OH - C3 - OS
Could not find angle parameter: OH - C3 - C3
Could not find angle parameter: OH - C3 - H2
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: O - P5 - O
Could not find angle parameter: O - P5 - O
Could not find angle parameter: O - P5 - OS
Could not find angle parameter: NB - CA - H5
Could not find angle parameter: NB - CA - NB
Could not find angle parameter: NB - CA - NH
Could not find angle parameter: NB - CA - CA
Could not find angle parameter: C3 - OS - C3
Could not find angle parameter: C3 - OH - HO
Could not find angle parameter: C3 - C3 - C3
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - OH
Could not find angle parameter: C3 - NA - CD
Could not find angle parameter: C3 - NA - CA
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - NA
Could not find angle parameter: C3 - C3 - H2
Could not find angle parameter: OH - C3 - H1
Could not find angle parameter: C3 - OH - HO
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: OS - C3 - NA
Could not find angle parameter: OS - C3 - H2
Could not find angle parameter: OS - C3 - C3
Could not find angle parameter: OS - C3 - C3
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: C3 - OS - C3
Could not find angle parameter: C3 - C3 - OH
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: OS - C3 - C3
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: OS - C3 - H1
Could not find angle parameter: OS - P5 - O
Could not find angle parameter: OS - P5 - O
Could not find angle parameter: C3 - C3 - OS
Could not find angle parameter: C3 - C3 - C3
Could not find angle parameter: C3 - C3 - H1
Could not find angle parameter: P5 - OS - C3
Could not find angle parameter: P5 - OS - C3
Building proper torsion parameters.
** No torsion terms for O2-C-O2-C3
** No torsion terms for O2-C3-C3-NA
** No torsion terms for O2-C3-C3-H2
** No torsion terms for O2-C3-C3-OS
** No torsion terms for C-O2-C3-C3
** No torsion terms for C-O2-C3-H1
** No torsion terms for CT-C-O2-C3
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H2-C3-C3-H1
** No torsion terms for HO-OH-C3-H1
** No torsion terms for HO-OH-C3-H1
** No torsion terms for HO-OH-C3-H2
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H1-C3-OH-HO
** No torsion terms for H1-C3-C3-H1
** No torsion terms for H2-C3-C3-H1
** No torsion terms for NA-C3-C3-H1
** No torsion terms for CD-NA-C3-H2
** No torsion terms for CA-NB-CA-H5
** No torsion terms for OS-C3-C3-H1
** No torsion terms for C3-C3-C3-H1
** No torsion terms for CA-CA-NH-HN
** No torsion terms for CA-CA-NH-HN
** No torsion terms for CA-NC-CD-NA
** No torsion terms for CA-NC-CD-H5
** No torsion terms for OS-C3-C3-OS
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-OH-HO
** No torsion terms for OS-C3-C3-H1
** No torsion terms for C3-OS-C3-H2
** No torsion terms for C3-C3-OH-HO
** No torsion terms for C3-C3-C3-H1
** No torsion terms for CA-NA-CD-H5
** No torsion terms for CA-NA-CD-NC
** No torsion terms for CA-NA-C3-H2
** No torsion terms for CA-NB-CA-H5
** No torsion terms for OH-C3-C3-C3
** No torsion terms for OH-C3-C3-OS
** No torsion terms for OH-C3-C3-H1
** No torsion terms for OH-C3-C3-H1
** No torsion terms for OS-P5-OS-C3
** No torsion terms for NB-CA-NB-CA
** No torsion terms for C3-C3-C3-OS
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-C3-OH-HO
** No torsion terms for C3-C3-C3-OS
** No torsion terms for C3-C3-C3-H2
** No torsion terms for OH-C3-C3-C3
** No torsion terms for OH-C3-C3-OH
** No torsion terms for OH-C3-C3-H1
** No torsion terms for OH-C3-C3-OS
** No torsion terms for OH-C3-C3-H2
** No torsion terms for O-P5-OS-C3
** No torsion terms for C3-C3-C3-C3
** No torsion terms for C3-C3-C3-OS
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-C3-OH-HO
** No torsion terms for C3-C3-OS-C3
** No torsion terms for C3-C3-OH-HO
** No torsion terms for CA-NB-CA-CA
** No torsion terms for CA-NB-CA-NA
** No torsion terms for CA-NB-CA-NH
** No torsion terms for CA-NB-CA-CA
** No torsion terms for OH-C3-OS-C3
** No torsion terms for OH-C3-C3-C3
** No torsion terms for OH-C3-C3-H1
** No torsion terms for OH-C3-C3-OH
** No torsion terms for O-P5-OS-C3
** No torsion terms for NB-CA-NB-CA
** No torsion terms for NB-CA-NH-HN
** No torsion terms for NB-CA-NH-HN
** No torsion terms for C3-OS-C3-C3
** No torsion terms for C3-OS-C3-H1
** No torsion terms for C3-OS-C3-C3
** No torsion terms for C3-C3-C3-C3
** No torsion terms for C3-C3-C3-OH
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-C3-OH-HO
** No torsion terms for C3-NA-CD-H5
** No torsion terms for C3-NA-CD-NC
** No torsion terms for C3-OS-C3-H1
** No torsion terms for C3-C3-NA-CD
** No torsion terms for C3-C3-NA-CA
** No torsion terms for OH-C3-C3-H1
** No torsion terms for C3-C3-OS-C3
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-C3-C3-H1
** No torsion terms for OS-C3-NA-CD
** No torsion terms for OS-C3-NA-CA
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-C3-OH
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-C3-H1
** No torsion terms for OS-C3-C3-H1
** No torsion terms for C3-OS-C3-NA
** No torsion terms for C3-OS-C3-H2
** No torsion terms for C3-OS-C3-C3
** No torsion terms for C3-C3-OH-HO
** No torsion terms for OS-C3-C3-OS
** No torsion terms for OS-C3-C3-C3
** No torsion terms for OS-C3-C3-H1
** No torsion terms for C3-C3-OS-C3
** No torsion terms for C3-C3-C3-OH
** No torsion terms for C3-C3-C3-H1
** No torsion terms for C3-OS-P5-O
** No torsion terms for C3-OS-P5-OS
** No torsion terms for C3-OS-P5-O
** No torsion terms for P5-OS-P5-OS
** No torsion terms for P5-OS-P5-O
** No torsion terms for P5-OS-P5-O
** No torsion terms for P5-OS-C3-H1
** No torsion terms for P5-OS-C3-H1
** No torsion terms for P5-OS-C3-C3
** No torsion terms for P5-OS-C3-C3
** No torsion terms for P5-OS-C3-H1
** No torsion terms for P5-OS-C3-H1
** No torsion terms for P5-OS-P5-O
** No torsion terms for P5-OS-P5-OS
** No torsion terms for P5-OS-P5-O
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for CD-CA-NA-C3
atoms are: C8 C4 N9 C1'
** Warning: No sp2 improper torsion term for NA-H5-CD-NC
atoms are: N9 H8 C8 N7
** Warning: No sp2 improper torsion term for NH-CA-CA-NB
atoms are: N6 C5 C6 N1
** Warning: No sp2 improper torsion term for CA-NC-CA-CA
atoms are: C6 N7 C5 C4
** Warning: No sp2 improper torsion term for CA-NA-CA-NB
atoms are: C5 N9 C4 N3
total 39 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
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Received on Mon Dec 15 2014 - 15:00:02 PST
