Dar all amber users,
I want to simulate the complex with pdbid: 3jbi
This is my tleap script:
tleap -s -f /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB
loadamberparams frcmod.ionsjc_tip3p
loadamberparams frcmod.phos
loadamberprep ADP.prep
loadamberparams frcmod.magnesium
loadamberprep magnesium.prep
pdb = loadpdb test.pdb
alignaxes pdb
center pdb
solvateBOX pdb TIP3PBOX 12.0
charge pdb
addions pdb Na+ 0
saveamberparm pdb prova.prmtop prova.rst7
and I have the following errors:
Could not find bond parameter for: O - MG
Could not find bond parameter for: O2 - MG
Could not find bond parameter for: O2 - MG
Could not find bond parameter for: MG - O3
Could not find bond parameter for: MG - O3
Could not find bond parameter for: MG - O3
Building angle parameters.
Could not find angle parameter: O - MG - O3
Could not find angle parameter: O - MG - O2
Could not find angle parameter: O - MG - O2
Could not find angle parameter: O - MG - O3
Could not find angle parameter: O - MG - O3
Could not find angle parameter: C - O - MG
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: O2 - MG - O2
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: O2 - MG - O3
Could not find angle parameter: CO - O2 - MG
Could not find angle parameter: CO - O2 - MG
Could not find angle parameter: MG - O3 - P
Could not find angle parameter: MG - O3 - P
Could not find angle parameter: MG - O3 - P
Could not find angle parameter: O3 - MG - O3
Could not find angle parameter: O3 - MG - O3
Could not find angle parameter: O3 - MG - O3
Building proper torsion parameters.
1-4: angle 2311 2312 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 2310 7759 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 7759 7761 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 7759 7761 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 7762 7763 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 7760 7762 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 7760 7763 duplicates bond ('triangular' bond) or angle ('square'
bond)
** No torsion terms for O-MG-O3-P
** No torsion terms for O-MG-O2-CO
** No torsion terms for O-MG-O2-CO
** No torsion terms for O-MG-O3-P
** No torsion terms for O-MG-O3-P
** No torsion terms for C-O-MG-O3
** No torsion terms for C-O-MG-O2
** No torsion terms for C-O-MG-O2
** No torsion terms for C-O-MG-O3
** No torsion terms for C-O-MG-O3
** No torsion terms for O2-CO-O2-MG
** No torsion terms for O2-MG-O3-P
** No torsion terms for O2-MG-O3-P
** No torsion terms for O2-MG-O3-P
** No torsion terms for O2-CO-O2-MG
** No torsion terms for O2-MG-O3-P
** No torsion terms for O2-MG-O3-P
** No torsion terms for O2-MG-O3-P
** No torsion terms for CO-O2-MG-O3
** No torsion terms for CO-O2-MG-O2
** No torsion terms for CO-O2-MG-O3
** No torsion terms for CO-O2-MG-O3
** No torsion terms for CO-O2-MG-O3
** No torsion terms for CO-O2-MG-O2
** No torsion terms for CO-O2-MG-O3
** No torsion terms for CO-O2-MG-O3
** No torsion terms for 2C-CO-O2-MG
** No torsion terms for 2C-CO-O2-MG
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-OS
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-OS
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-OS
** No torsion terms for P-O3-MG-O3
** No torsion terms for P-O3-MG-O3
** No torsion terms for P-O3-MG-O3
** No torsion terms for P-O3-MG-O3
** No torsion terms for O3-MG-O3-P
** No torsion terms for O3-MG-O3-P
Building improper torsion parameters.
old PREP-specified impropers:
<adp 504>: C8 C4 N9 C1*
<adp 504>: C6 H60 N6 H61
<adp 504>: N7 N9 C8 H80
<adp 504>: N1 N3 C2 H2
<adp 504>: C5 N1 C6 N6
total 1469 improper torsions applied
5 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Any suggestions will be highly appreciated.
Thank you so much
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Received on Wed May 10 2017 - 06:00:04 PDT
