[AMBER] Tleap naming problem

From: Rui Chen <rchen6.ualberta.ca>
Date: Wed, 25 Dec 2019 20:53:49 -0700


I am preparing a protein/ligand complex for MD simulation.

I used:
1. "antechamber -i rui_6058.out -fi gout -o 6058_rep2_pose1.mol2 -fo mol2
-c esp" this command to generate the mol2 file; (rui_6058.out is the
Gaussian output file, the files begin with 6058_rep2_pose1 is a small
molecule or ligand alone)
2. "parmchk -i 6058_rep2_pose1.mol2 -f mol2 -o 6058_rep2_pose1.frcmod"
command to generate the missing parameters;
3. Then I used Tleap to save the library of the ligand. I realized the
residue name of the ligand was changed to MOL. So I modified the
protein/ligand complex PDB file, also change the ligand residue name to
match the library.
4. When I load the protein/ligand complex PDB file into Tleap, I got
error. Unknown
residue: MOL (I also tried not to change the ligand name, I got the same
error, Unknown residue: L)

Could you help me solve the problem? I attached all the related files here.
Thank you.

Best regards,

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Received on Wed Dec 25 2019 - 20:00:02 PST
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