In fact, both tleap and teLeap are in the ~/amber20/bin/ directory as shown below, when I typed on the command line as below:
zhangl:~/amber20/bin$ ls -l t*p
-rwxrwxrwx 1 root root 994208 Apr 27 2021 teLeap
-rwxrwxrwx 1 root root 272 Apr 27 2021 tleap
zhangl:~/amber20/bin$ ./teLeap
Welcome to LEaP!
(no leaprc in search path)
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
lzhang:~/amber20/bin$ ./tleap
-I: Adding /home/amber20/dat/leap/prep to search path.
-I: Adding /home/amber20/dat/leap/lib to search path.
-I: Adding /home/amber20/dat/leap/parm to search path.
-I: Adding /home/amber20/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
>
When I ran the set up step, I typed "tleap -f 03.leap.sh" on the command line.
Also, previously I used the same command to set up other simple simulation system (including one protein and one small ligand) without any issue. On the screen, it also showed teLeap line but it finished the setting up without any error. So I am not sure where was really wrong.
In fact, I did not cap the first residue and last residue of the proteins before the set up step. But do I really need to do that? Can any program or chimera do that? Thanks.
Laura
________________________________
From: aishen via AMBER <amber.ambermd.org>
Sent: Saturday, December 3, 2022 20:06
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] about setting up a simulation system including multiple protein
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C7fb575120538434983d008dad593bfc9%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638057127841291964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=l1Hwar5MzvsgMleeip5QS1OepbbLbFxW889HAIZE%2BvM%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C7fb575120538434983d008dad593bfc9%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638057127841291964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=l1Hwar5MzvsgMleeip5QS1OepbbLbFxW889HAIZE%2BvM%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 03 2022 - 19:00:03 PST
