Re: [AMBER] Simulating drug molecules in lipid bilayers

From: Dickson, Callum <>
Date: Wed, 13 Jun 2018 23:24:22 +0000

Hi Christopher,

You can use cpptraj to get a pdb of the final frame of your run (after imaging the bilayer). Once you have a pdb of the equilibrated bilayer you need to re-number the residues to keep with the amber format:

PA 1
PC 1
OL 1
PA 2
PC 2
OL 2

...etc. I have a simple script somewhere I can find if you need help with that.

To add a pdb of your drug molecule, there is a script in this tutorial:

This will position the drug a defined z-distance from the center of the bilayer.

Again, let me know questions in regards to that.


-----Original Message-----
From: Christopher Faulkner []
Sent: Tuesday, June 12, 2018 8:30 AM
Subject: [AMBER] Simulating drug molecules in lipid bilayers

Dear Amber users,

I built some lipid systems using charmm gui and converted them to amber lipid format using the script. I have simulated them to the desired amount of time and I am now interested in adding some small drug molecules to the systems. Does anybody know how I can take the equilibrated coordinates from the pure lipid simulations and add the drug molecules to them and retain the lipid14 format so I can simulate the combined systems? I have the pdb files for the drug molecules and their parameters were generated using AMBER GAFF.

Any help is much appreciated.


Christopher Faulkner

PhD student

Cardiff University

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Received on Wed Jun 13 2018 - 16:30:02 PDT
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