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

From: Min Chiang Gary Ong <minchiao.ucr.edu>
Date: Wed, 19 May 2021 06:24:13 -0700


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.


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Received on Wed May 19 2021 - 06:30:03 PDT
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