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
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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 (stellvertretende Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
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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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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 Thu Jun 19 2025 - 00:30:02 PDT
