Hi Pengfei,
Thanks so much. So do you mean that I should use the actual hydrogen atom
itself after LEAP adds them?
Thanks,
Naiem
Naiem T. Issa, Ph.D
M.D. Candidate Class of 2017
Georgetown University School of Medicine
Howard Hughes Biomedical Research Scholar
Tel: 703.587.1315 E-mail: nti.georgetown.edu
On Fri, Feb 10, 2017 at 3:50 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Naiem,
>
> Based on your error, I think it is wrong to use these commands:
>
> > bond MOL.261.ZN MOL.94.ND1
> > bond MOL.261.ZN MOL.96.ND1
> > bond MOL.261.ZN MOL.119.NE2
>
>
> The atoms bond to ZN should not be atoms with hydrogen on them (but NA
> atom type is).
>
> So please check whether these bonds are correct.
>
> Kind regards,
> Pengfei
>
> > On Feb 10, 2017, at 2:43 PM, Naiem Issa <nti.georgetown.edu> wrote:
> >
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Feb 10 2017 - 13:30:03 PST
