Re: [AMBER] Tleap naming problem

From: David Case <>
Date: Thu, 2 Jan 2020 13:30:41 +0000

On Wed, Jan 01, 2020, Rui Chen wrote:
>I am preparing the protein/ligand complex system to run MD simulation
>I order to make the Tleap understand my ligand, I prepared the mol2 file,
>the frcmod file and the ligand library file. According to your suggestion,
>I used "antechamber -i rui_6058.out -fi gout -o 6058_rep2_pose1.mol2 -fo
>mol2 -c esp -rn L" and "parmchk -i 6058_rep2_pose1.mol2 -f mol2 -o
>6058_rep2_pose1.frcmod" commands. I also used "desc" and "list" to check.

Can you say what happened without asking people to download a number of
files and try to go through each one? In particular, you post two
different tleap*.in files, but just one leap.log file; also you have
several PDB files, and it can take quite a while to figure out which one
was used.

The error in the leap.log file is this:

FATAL: Atom .R<L 0>.A<O4 41> does not have a type.
FATAL: Atom .R<L 0>.A<O5 42> does not have a type.

There is also this message:

Created a new atom named: O4 within residue: .R<L 0>
Created a new atom named: O5 within residue: .R<L 0>

That should give a big clue to you: leap doesn't know the atom type for
atom O4. Looking in the mol2 file (or, I presume, in the L.lig file),
you will see that there is no O4 atom defined: you basic problem seems
to be that that atom names in the input PDB file don't match those in
the mol2 file. You have to fix that.

Try to work in small steps: just make a ligand file first, with no
protein or solvent. Look carefully at messages like the above in the
leap.log file, and try to think about why you might be getting them.


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Received on Thu Jan 02 2020 - 06:00:02 PST
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