Dear Amber Users,
I am trying to model a protein with two Zn ions (One coordinated with 4
CYS whereas the other coordinated with 2 CYS and 2 HIS (one in HIE and one
in HID protonation states)). I saw that Zn with 4 CYS can be modelled using
Center ID 1 from ZAFF. The closest I can find for other Zn is Center ID 4.
when I model the system, tleap throws, lengths, angles & torsions are
missing for interactions containing two Zn.
TLEAP SCRIPT:
tleap -s
source leaprc.protein.ff14SB
addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } { "N2" "N" "sp3" } }
loadoff atomic_ions.lib
source leaprc.water.tip3p
loadamberprep ZAFF.prep
loadamberparams ZAFF.frcmod
x = loadpdb prepped_zaff_named.pdb
bond x.45.ZN x.3.SG
bond x.45.ZN x.6.SG
bond x.45.ZN x.26.SG
bond x.45.ZN x.29.SG
bond x.46.ZN x.17.SG
bond x.46.ZN x.20.SG
bond x.46.ZN x.35.NE2
bond x.46.ZN x.38.ND1
solvatebox x TIP3PBOX 12.0
addions x NA 0
savepdb x try_solv.pdb
saveamberparm x protein.prmtop protein.inpcrd
quit
ERROR :
Error: Could not find bond parameter for: ZN - ZN
Building angle parameters.
Error: Could not find angle parameter: S1 - ZN - ZN
Error: Could not find angle parameter: S1 - ZN - ZN
Error: Could not find angle parameter: S4 - ZN - ZN
Error: Could not find angle parameter: S4 - ZN - N7
Error: Could not find angle parameter: S4 - ZN - ZN
Error: Could not find angle parameter: S4 - ZN - N7
Error: Could not find angle parameter: S1 - ZN - ZN
Error: Could not find angle parameter: S1 - ZN - ZN
Error: Could not find angle parameter: N3 - ZN - ZN
Error: Could not find angle parameter: N3 - ZN - N7
Error: Could not find angle parameter: N7 - ZN - ZN
Building proper torsion parameters.
Error: ** No torsion terms for S1-ZN-ZN-S4
Error: ** No torsion terms for S1-ZN-ZN-S4
Error: ** No torsion terms for S1-ZN-ZN-N3
Error: ** No torsion terms for S1-ZN-ZN-N7
Error: ** No torsion terms for CT-S1-ZN-ZN
Error: ** No torsion terms for S1-ZN-ZN-S4
Error: ** No torsion terms for S1-ZN-ZN-S4
Error: ** No torsion terms for S1-ZN-ZN-N3
Error: ** No torsion terms for S1-ZN-ZN-N7
Error: ** No torsion terms for CT-S1-ZN-ZN
Error: ** No torsion terms for S4-ZN-ZN-S1
Error: ** No torsion terms for S4-ZN-ZN-S1
Error: ** No torsion terms for S4-ZN-N7-CC
Error: ** No torsion terms for S4-ZN-N7-CR
Error: ** No torsion terms for CT-S4-ZN-ZN
Error: ** No torsion terms for CT-S4-ZN-N7
Error: ** No torsion terms for S4-ZN-ZN-S1
Error: ** No torsion terms for S4-ZN-ZN-S1
Error: ** No torsion terms for S4-ZN-N7-CC
Error: ** No torsion terms for S4-ZN-N7-CR
Error: ** No torsion terms for CT-S4-ZN-ZN
Error: ** No torsion terms for CT-S4-ZN-N7
Error: ** No torsion terms for S1-ZN-ZN-N3
Error: ** No torsion terms for S1-ZN-ZN-N7
Error: ** No torsion terms for CT-S1-ZN-ZN
Error: ** No torsion terms for S1-ZN-ZN-N3
Error: ** No torsion terms for S1-ZN-ZN-N7
Error: ** No torsion terms for CT-S1-ZN-ZN
Error: ** No torsion terms for CV-N3-ZN-ZN
Error: ** No torsion terms for CV-N3-ZN-N7
Error: ** No torsion terms for N3-ZN-N7-CC
Error: ** No torsion terms for N3-ZN-N7-CR
Error: ** No torsion terms for CR-N3-ZN-ZN
Error: ** No torsion terms for CR-N3-ZN-N7
Error: ** No torsion terms for CR-N7-ZN-ZN
Error: ** No torsion terms for CC-N7-ZN-ZN
I two Zn are away and are not bonded. Why is tleap asking for these bonded
parameters?
What is the best way to model this system?
Any help is appreciated.
Regards,
Aravind R
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Received on Sat Dec 11 2021 - 02:30:02 PST
