Look at your error file.
Do you see where it says:
Warning: There is a bond of 31.125234 angstroms between:
Error: Could not find bond parameter for: ZN - ZN
To me that says that for some reason your ZN is bonded to another ZN.
Maria
> On Oct 21, 2021, at 4:48 PM, Daniel Hall <D.Hall1.bradford.ac.uk> wrote:
>
> Hello All,
>
> I am trying to simulate a zinc finger (ZnF) using the bonded method as described in the ZAFF tutorial https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
>
> I have managed to simulate my protein with a single ZnF domain, but when I tried to simulate with three tandem ZnF domains, I got the following error message when I tried to save the prmtop and inpcrd files:
>
> Checking Unit.
>
> Warning: There is a bond of 31.125234 angstroms between:
>
> Warning: There is a bond of 45.856460 angstroms between:
>
> Note: Ignoring the warnings from Unit Checking.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> Error: Could not find bond parameter for: ZN - ZN
>
> Error: Could not find bond parameter for: ZN - ZN
> Building angle parameters.
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: S4 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: N3 - ZN - ZN
>
> Error: Could not find angle parameter: ZN - ZN - ZN
> Building proper torsion parameters.
>
> Error: ** No torsion terms for S4-ZN-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-ZN
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-S4
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for S4-ZN-ZN-N3
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-ZN
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-S4
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for N3-ZN-ZN-N3
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CT-S4-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for CV-N3-ZN-ZN
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
>
> Error: ** No torsion terms for CR-N3-ZN-ZN
> 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
> old PREP-specified impropers:
> <CY4 3>: -M CA N HN
> <CY4 3>: CA +M C O
> <CY4 8>: -M CA N HN
> <CY4 8>: CA +M C O
> <HD2 21>: -M CA N H
> <HD2 21>: CA +M C O
> <HD2 21>: CG CE1 ND1 HD1
> <HD2 21>: CG NE2 CD2 HD2
> <HD2 21>: ND1 NE2 CE1 HE1
> <HD2 21>: ND1 CD2 CG CB
> <HD2 25>: -M CA N H
> <HD2 25>: CA +M C O
> <HD2 25>: CG CE1 ND1 HD1
> <HD2 25>: CG NE2 CD2 HD2
> <HD2 25>: ND1 NE2 CE1 HE1
> <HD2 25>: ND1 CD2 CG CB
> <CY4 33>: -M CA N HN
> <CY4 33>: CA +M C O
> <CY4 38>: -M CA N HN
> <CY4 38>: CA +M C O
> <HD2 51>: -M CA N H
> <HD2 51>: CA +M C O
> <HD2 51>: CG CE1 ND1 HD1
> <HD2 51>: CG NE2 CD2 HD2
> <HD2 51>: ND1 NE2 CE1 HE1
> <HD2 51>: ND1 CD2 CG CB
> <HD2 55>: -M CA N H
> <HD2 55>: CA +M C O
> <HD2 55>: CG CE1 ND1 HD1
> <HD2 55>: CG NE2 CD2 HD2
> <HD2 55>: ND1 NE2 CE1 HE1
> <HD2 55>: ND1 CD2 CG CB
> <CY4 63>: -M CA N HN
> <CY4 63>: CA +M C O
> <CY4 66>: -M CA N HN
> <CY4 66>: CA +M C O
> <HD2 79>: -M CA N H
> <HD2 79>: CA +M C O
> <HD2 79>: CG CE1 ND1 HD1
> <HD2 79>: CG NE2 CD2 HD2
> <HD2 79>: ND1 NE2 CE1 HE1
> <HD2 79>: ND1 CD2 CG CB
> <HD2 83>: -M CA N H
> <HD2 83>: CA +M C O
> <HD2 83>: CG CE1 ND1 HD1
> <HD2 83>: CG NE2 CD2 HD2
> <HD2 83>: ND1 NE2 CE1 HE1
> <HD2 83>: ND1 CD2 CG CB
> total 300 improper torsions applied
> 48 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> Warning: Parameter file was not saved.
>
>
>
> My tleap in file is as follows:
>
> source oldff/leaprc.ff99SBildn
> source leaprc.water.tip3p
> loadamberparams frcmod.ions234lm_1264_tip3p
> addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } { "N2" "N" "sp3" } }
> loadamberprep ZAFF.prep
> loadamberparams ZAFF.frcmod
> mol = loadpdb Sp1_amber.pdb
> bond mol.86.ZN mol.3.SG
> bond mol.86.ZN mol.8.SG
> bond mol.86.ZN mol.21.NE2
> bond mol.86.ZN mol.25.NE2
> bond mol.84.ZN mol.33.SG
> bond mol.84.ZN mol.38.SG
> bond mol.84.ZN mol.51.NE2
> bond mol.84.ZN mol.55.NE2
> bond mol.85.ZN mol.66.SG
> bond mol.85.ZN mol.63.SG
> bond mol.85.ZN mol.83.NE2
> bond mol.85.ZN mol.79.NE2
> solvateOct mol TIP3PBOX 16
> addions mol Cl- 0
> savepdb mol Sp1_solv.pdb
> saveamberparm mol Sp1_solv.prmtop Sp1_solv.inpcrd
> quit
>
>
> Any help or guidance will be much appreciated
>
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Received on Tue Oct 26 2021 - 17:30:03 PDT
