Hi Callum,
This is really helpful, I can write my own script to do the re-number. The com_placement.py script works really well and I have done a test simulation which all seems to working so thank you very much for you suggestion.
Regards,
Christopher
________________________________
From: Dickson, Callum <callum.dickson.novartis.com>
Sent: 14 June 2018 00:24:22
To: AMBER Mailing List
Subject: Re: [AMBER] Simulating drug molecules in lipid bilayers
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 Thu Jun 14 2018 - 03:00:02 PDT
