In fact, I found out where was wrong. I had a typo before loading the protein pdb file. After removing the typo, I solved the issue. Thank you very much for helping!
Laura
________________________________
From: laura zhang via AMBER <amber.ambermd.org>
Sent: Saturday, December 3, 2022 20:44
To: aishen <aishen.free.fr>; AMBER Mailing List <amber.ambermd.org>; Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Subject: Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein
I changed CYS into CYX, but I still got error at the end as shown below:
...
/home/amber20/bin/teLeap: Fatal Error!
Error from the parser: syntax error
Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
I am not sure where was still wrong.
________________________________
From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Sent: Saturday, December 3, 2022 20:37
To: aishen <aishen.free.fr>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein
Did you make sure the disulfide-linked cysteine residues are named CYX in the PDB? That is the residue name tleap expects you to use instead of CYS for disulfide-linked cysteines.
Best,
Matthew
> On Dec 3, 2022, at 8:06 PM, aishen via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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 - 18:30:02 PST
