it's not teleap it's tleap
Le 04/12/2022 à 01:36, laura zhang via AMBER a écrit :
> Dear all,
>
> I tried to set up an amber simulation system which has 3 proteins and one small ligand. I did energy minimization on each protein using chimera before run tleap step to set up the system. But I still got a lot of error message like below,
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> /home/amber20/bin/teLeap: Error!
> Could not find bond parameter for: SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find bond parameter for: SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find bond parameter for: SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find bond parameter for: SH - SH
> Building angle parameters.
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: 2C - SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: SH - SH - 2C
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: SH - SH - HS
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: HS - SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: 2C - SH - SH
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: SH - SH - 2C
>
> /home/amber20/bin/teLeap: Error!
> Could not find angle parameter: SH - SH - HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for 2C-SH-SH-HS
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-2C
>
> /home/amber20/bin/teLeap: Error!
> ** No torsion terms for HS-SH-SH-HS
> Building improper torsion parameters.
> total 1146 improper torsions applied
>
> The following is the copy of part of the tleap input file:
>
> rec=loadpdb ./tg2_min.pdb
>
> bond rec.36.SG rec.110.SG
> bond rec.51.SG rec.60.SG
>
> ###load ligand frcmod/mol2
> loadamberparams ./nag_ligand.frcmod
> lg1=loadmol2 ./nag_antechamber.mol2
>
> lg2=loadpdb ./scfv1_min.pdb
>
> bond lg2.24.SG lg2.98.SG
>
> lg3=loadpdb ./scfv2_min.pdb
>
> bond lg3.161.SG lg3.226.SG
>
> ###create gase-phase complex
> gascomplex= combine {rec lg1 lg2 lg3}
>
> ###write gas-phase pdb
> savepdb gascomplex tg2.gas.complex.pdb
>
> ###write gase-phase toplogy and coord files for MMGBSA calc
> saveamberparm gascomplex tg2.complex.parm7 tg2.gas.complex.rst7
> saveamberparm rec tg2.gas.receptor.parm7 tg2.gas.receptor.rst7
> saveamberparm lg1 tg2.gas.lg1.parm7 tg2.gas.lg1.rst7
> saveamberparm lg2 tg2.gas.lg2.parm7 tg2.gas.lg2.rst7
> saveamberparm lg3 tg2.gas.lg3.parm7 tg2.gas.lg3.rst7
>
> I am wondering how to solve the above problems. Thank you very much.
>
> Laura
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Received on Sat Dec 03 2022 - 17:30:03 PST
