Hi Stephan,
Thank you for the update. I don’t need the fix urgently, but let me know once it is done. That is good to know about the CompEL protocols – I wasn’t aware that Amber didn’t have one yet. I’ll play around with the Gromacs one after I build the double bilayer.
Best,
Kendall
From: Stephan Schott <s.schott-verdugo.fz-juelich.de>
Date: Friday, June 20, 2025 at 6:48 AM
To: Cherry, Kendall <kche.email.unc.edu>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building double bilayer using packmol-memgen
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Hi Kendall,
Thanks for the report. As there is not many people using the option, there is indeed an issue with how I am keeping track of the pdb input there which I did not pick up in my internal testing and is still a bug in the latest release, so it is great to have someone playing around with it. Be aware that we do not have a real CompEL approach in Amber afaik, but one could use the input files for the Gromacs protocol. I am passing a patch next week, so this is a good opportunity to fix this one as well. I can let you know once that is done.
If you need things more urgently, let me know, and I can send you a patch to fix this in a local version you might have available.
Best regards,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
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Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
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El jue, 19 jun 2025 a la(s) 3:49 p.m., Cherry, Kendall (kche.email.unc.edu<mailto:kche.email.unc.edu>) escribió:
Hi Stephan,
Yes, I am using Amber 24, with Packmol-Memgen version 2024.3.27.
Thanks,
Kendall Cherry
From: Stephan Schott <s.schott-verdugo.fz-juelich.de<mailto:s.schott-verdugo.fz-juelich.de>>
Date: Thursday, June 19, 2025 at 3:25 AM
To: Cherry, Kendall <kche.email.unc.edu<mailto:kche.email.unc.edu>>, AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] Building double bilayer using packmol-memgen
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Hi Kendall,
Can you tell me which version that is?
Best regards,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellvertretende Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Cherry, Kendall via AMBER <
amber.ambermd.org<mailto:
amber.ambermd.org>> schrieb am Mo., 16. Juni 2025, 18:32:
Hello,
I work with membrane proteins and am interested in creating a double bilayer system to study ion flux through the protein. I have successfully built a single bilayer system using packmol-memgen, but when I add the computational electrophysiology flags (--double --charge_imbalance 2 --imbalance_ion cat), I get this error:
Traceback (most recent call last):
File "/proj/pierilab/software/amber/amber24/bin/packmol-memgen", line 193, in <module>
pmg.run_all()
File "/proj/pierilab/software/amber/amber24/lib/python3.12/site-packages/packmol_memgen/main.py", line 2005, in run_all
pack = self.prepare()
^^^^^^^^^^^^^^
File "/proj/pierilab/software/amber/amber24/lib/python3.12/site-packages/packmol_memgen/main.py", line 1358, in prepare
solvent_vol_up = (X_len*Y_len*(abs(Z_dim[bilayer][1])-leaflet_z))-solvol[bilayer][1]
~~~~~~^^^^^^^^^
IndexError: list index out of range
I have reproduced this error with the --double flag alone, so it is not due to the --charge_imbalance or --imbalance_ion flags. I also have tried changing the dimensions of the box (either --distxy_fix 75 --dist_wat 25 or --dims 75 75 200 ) just to see if that fixes this issue, but it does not. This is my full packmol-memgen command:
packmol-memgen --pdb LLLL_tleap.pdb --lipids POPC --dims 75 75 200 --random --nloop 30 --salt --keepligs --ffwat opc --ffprot ff19SB --notprotonate --nottrim --double
I would welcome help from anyone who knows packmol-memgen better than I do, and/or anyone who has successfully built a double bilayer system!
Thank you,
Kendall Cherry
Chemistry Ph.D. Student
University of North Carolina at Chapel Hill
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
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Received on Fri Jun 20 2025 - 04:30:02 PDT
