Re: [AMBER] Tleap naming problem

From: David Case <>
Date: Thu, 26 Dec 2019 14:35:43 +0000

On Wed, Dec 25, 2019, Rui Chen wrote:
>I am preparing a protein/ligand complex for MD simulation.
>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)

You can (and probably should) use the "-rn" flag to set the residue name
you want.

>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.

It's not clear exactly what you did here, or why. Having a mol2 file
(from step 1) and a frcmod file (from step 2) is all you need.

Use the tleap loadMol2 command to load your ligand; use the "list"
command in tleap to make sure it has the name you expect, and the "desc"
command to examine what is in it (if you need to).

>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)

The "list" command in tleap is your friend: it can tell you at each step
what residues leap knows about.


p.s.: on a brief glance, it looks like your file calls the
ligand "L", wheras the pdb file calls the ligand "MOL".

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Received on Thu Dec 26 2019 - 07:00:01 PST
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