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

From: David A Case <>
Date: Wed, 19 May 2021 13:22:23 -0400

On Wed, May 19, 2021, Min Chiang Gary Ong wrote:
>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.

Can you say exactly what you did in VMD? The inputs to VMD should be your
prmtop file and inpcrd file (both created by the saveAmberParm command in
tleap.). The phrase "visualize it with VMD with the PDB" is pretty vague:
what is "it" in this context, and what you do mean by "with the PDB".?

Your approach looks OK...let's hope it's just a VMD problem.


p.s. if it doesn't seem to be VMD, you can try this: use ambpdb to create a
PDB file from your prmtop/inpcrd pair. Use a text editor to compare to your
starting dimer structure, or just load this new PDB file into VMD. And/or:
use the checkstructure option in cpptraj to look for bad bonds and contacts.

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Received on Wed May 19 2021 - 10:30:02 PDT
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