Re: [AMBER] Simulating drug molecules in lipid bilayers

From: Dickson, Callum <callum.dickson.novartis.com>
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
TER
PA 2
PC 2
OL 2
TER

...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 com_placement.py script in this tutorial:

https://github.com/callumjd/AMBER-Umbrella_COM_restraint_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.

Best,
Callum


-----Original Message-----
From: Christopher Faulkner [mailto:FaulknerC3.cardiff.ac.uk]
Sent: Tuesday, June 12, 2018 8:30 AM
To: amber.ambermd.org
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__charmmlipid2amber.py&d=DwICAg&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=dLp9cf_XD7gMSOvUHSEZ_LG95CIjGEUBWsTpWpGoGiw&s=jzFNUanvRNKUKojr6VFhldLaUdpWTYkIB3ygT55dKo4&e= 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.


Regards,


Christopher Faulkner

PhD student

Cardiff University



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