Hello,
I am trying to prepare topology & coordinates for my protein (PDBID: 4KUW,
carbonic anhydrase II) using ZAFF in LEAP. This crystal structure has a
4-coordinated Zn2+. I want to model it without the coordinating water at
this time (model system is completely devoid of water solvent for now). I
have read the ZAFF tutorial and revised the PDB file for Center ID #6 (
http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm) but am running
into an error (pasted at the end of this message). This is what I have done
in leap:
source leaprc.ff12SB
addAtomTypes { { "ZN" "Zn" "sp3" } ***I know part of the issue is here***
loadamberprep Full/Dir/To/ZAFF.prep
loadamberparams Full/Dir/To/ZAFF.frcmod
MOL=loadPDB revised_4KUW.pdb
bond MOL.261.ZN MOL.94.ND1
bond MOL.261.ZN MOL.96.ND1
bond MOL.261.ZN MOL.119.NE2
saveamberparm MOL testing.top testing.crd
I am not sure how to adjust the atom types since there are multiple
nitrogens. I also do not have the files atomic_ions.lib &
frcmod.ions1lsm_hfe_tip3p when I downloaded amber tools. Here is the error
output from the log file:
Checking Unit.
WARNING: There is a bond of 4.207668 angstroms between:
------- .R<HD4 94>.A<ND1 9> and .R<ZN6 261>.A<ZN 1>
WARNING: There is a bond of 4.271204 angstroms between:
------- .R<HD5 96>.A<ND1 9> and .R<ZN6 261>.A<ZN 1>
WARNING: There is a bond of 4.307543 angstroms between:
------- .R<HE2 119>.A<NE2 12> and .R<ZN6 261>.A<ZN 1>
ERROR: The unperturbed charge of the unit: 0.830080 is not integral.
WARNING: The unperturbed charge of the unit: 0.830080 is not zero.
-- ignoring the error and warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: NA - ZN
Could not find bond parameter for: NA - ZN
Could not find bond parameter for: NA - ZN
Building angle parameters.
Could not find angle parameter: N5 - ZN - NA
Could not find angle parameter: N5 - ZN - NA
Could not find angle parameter: CR - NA - ZN
Could not find angle parameter: H - NA - ZN
Could not find angle parameter: NA - ZN - N5
Could not find angle parameter: NA - ZN - N6
Could not find angle parameter: NA - ZN - NA
Could not find angle parameter: NA - ZN - NA
Could not find angle parameter: CC - NA - ZN
Could not find angle parameter: N6 - ZN - NA
Could not find angle parameter: CR - NA - ZN
Could not find angle parameter: H - NA - ZN
Could not find angle parameter: NA - ZN - N6
Could not find angle parameter: NA - ZN - NA
Could not find angle parameter: CC - NA - ZN
Could not find angle parameter: CW - NA - ZN
Could not find angle parameter: H - NA - ZN
Could not find angle parameter: CR - NA - ZN
Building proper torsion parameters.
1-4: angle 1415 4054 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1413 1417 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1452 4054 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1450 1454 duplicates bond ('triangular' bond) or angle ('square'
bond)
** No torsion terms for CV-N5-ZN-NA
** No torsion terms for CV-N5-ZN-NA
** No torsion terms for N5-ZN-NA-CC
** No torsion terms for N5-ZN-NA-H
** No torsion terms for N5-ZN-NA-CR
** No torsion terms for N5-ZN-NA-CR
** No torsion terms for N5-ZN-NA-H
** No torsion terms for N5-ZN-NA-CW
** No torsion terms for CR-NA-ZN-N5
** No torsion terms for CR-NA-ZN-N6
** No torsion terms for CR-NA-ZN-NA
** No torsion terms for CR-NA-ZN-NA
** No torsion terms for CR-N5-ZN-NA
** No torsion terms for CR-N5-ZN-NA
** No torsion terms for H-NA-ZN-N5
** No torsion terms for H-NA-ZN-N6
** No torsion terms for H-NA-ZN-NA
** No torsion terms for H-NA-ZN-NA
** No torsion terms for NA-ZN-N5-CR
** No torsion terms for NA-ZN-N5-CV
** No torsion terms for NA-ZN-N6-CR
** No torsion terms for NA-ZN-N6-CV
** No torsion terms for NA-ZN-NA-CC
** No torsion terms for NA-ZN-NA-H
** No torsion terms for NA-ZN-NA-CR
** No torsion terms for NA-ZN-NA-CR
** No torsion terms for NA-ZN-NA-H
** No torsion terms for NA-ZN-NA-CW
** No torsion terms for CC-NA-ZN-N5
** No torsion terms for CC-NA-ZN-N6
** No torsion terms for CC-NA-ZN-NA
** No torsion terms for CC-NA-ZN-NA
** No torsion terms for CV-N6-ZN-NA
** No torsion terms for N6-ZN-NA-CR
** No torsion terms for N6-ZN-NA-H
** No torsion terms for N6-ZN-NA-CW
** No torsion terms for CR-NA-ZN-N6
** No torsion terms for CR-NA-ZN-NA
** No torsion terms for CR-N6-ZN-NA
** No torsion terms for H-NA-ZN-N6
** No torsion terms for H-NA-ZN-NA
** No torsion terms for NA-ZN-N6-CR
** No torsion terms for NA-ZN-N6-CV
** No torsion terms for NA-ZN-NA-CR
** No torsion terms for NA-ZN-NA-H
** No torsion terms for NA-ZN-NA-CW
** No torsion terms for CC-NA-ZN-N6
** No torsion terms for CC-NA-ZN-NA
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 CC-CR-NA-ZN
atoms are: CG CE1 ND1 ZN
** Warning: No sp2 improper torsion term for CC-CR-NA-ZN
atoms are: CG CE1 ND1 ZN
** 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 CR-CW-NA-ZN
atoms are: CE1 CD2 NE2 ZN
** 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
old PREP-specified impropers:
<HD4 94>: -M CA N H
<HD4 94>: CA +M C O
<HD4 94>: CG CE1 ND1 HD1
<HD4 94>: CG NE2 CD2 HD2
<HD4 94>: ND1 NE2 CE1 HE1
<HD4 94>: ND1 CD2 CG CB
<HD5 96>: -M CA N H
<HD5 96>: CA +M C O
<HD5 96>: CG CE1 ND1 HD1
<HD5 96>: CG NE2 CD2 HD2
<HD5 96>: ND1 NE2 CE1 HE1
<HD5 96>: ND1 CD2 CG CB
<HE2 119>: -M CA N H
<HE2 119>: CA +M C O
<HE2 119>: CE1 CD2 NE2 HE2
<HE2 119>: CG NE2 CD2 HD2
<HE2 119>: ND1 NE2 CE1 HE1
<HE2 119>: ND1 CD2 CG CB
total 834 improper torsions applied
18 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Any guidance is appreciated. This will help me learn for other
Zn-containing proteins I'll need to model next.
Thanks,
Naiem
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Received on Fri Feb 10 2017 - 13:00:02 PST
