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 Thu Oct 21 2021 - 14:00:02 PDT
