Re: [AMBER] Tleap naming problem

From: Rui Chen <>
Date: Wed, 1 Jan 2020 14:19:00 -0700

Dear David,

I am preparing the protein/ligand complex system to run MD simulation
according to the following tutorial: .

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. I
still get fatal errors. I attach the input and output files here. Could you
please help me figure it out? Looking forward to your reply.

Best regards.

On Thu, Dec 26, 2019 at 7:36 AM David Case <> wrote:

> 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.
> ...dac
> 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 Wed Jan 01 2020 - 13:30:02 PST
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