Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand?

From: Carlos Simmerling <>
Date: Wed, 19 May 2021 12:19:40 -0400

I think it may be that you are loading the original pdb with the leap
prmtop. The atom order may not match. Try saving a pdb from inside leap and
using that with the prmtop for Vmd.

On Wed, May 19, 2021, 9:24 AM Min Chiang Gary Ong <> wrote:

> Hello,
> I am only interested in studying the interaction between 2 or more small
> molecules (no proteins).
> While I can generate the prmtop and inpcrd file for a single ligand with no
> issues, I struggle to make it work for multiple ligands. I am able to
> generate the prmtop file successfully, but when I tried to visualize it
> with VMD (load prmtop with the PDB file containing 2), the bonds are
> totally haywire.
> Attached is 'asphaltene.pdb' - the original small molecule which I can
> generate a prmtop successfully, 'asphaltene-dimer.pdb' is 2 of the same
> molecule in a same pdb file separated by TER and with different
> coordinates.
> I used tleap to generate my desired files as mentioned in the tutorial.
> source leaprc.gaff #Source leaprc file for gaff
> loadamberprep asphaltene.prepi #Load the prepi file for the ligand
> loadamberparams asphaltene.frcmod
> mol = loadpdb asphaltene_dimer.pdb #Load PDB file for protein-ligand
> complex
> saveamberparm mol asphaltene_test.prmtop asphaltene_test.inpcrd #Save AMBER
> topology and coordinate files
> quit #Quit tleap program
> The prepi and frcmod files are generated based on the single molecule PDB
> file. However, the prmtop file I obtained using the above commands gave me
> wrong results when I tried to visualize it with VMD with the PDB.
> Gary
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Received on Wed May 19 2021 - 09:30:02 PDT
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