Hi Seigo,
The default orientation of the protein is done with memembed, which should work for most cases. An alternative is to use the local opm/ppm version passing the --ppm flag, or orienting it manually with respect to the coordinate origin, and use the --preoriented flag.
I can have a look at your protein if you send it internally to me. That would help understand why things are not working as you expect.
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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yumura.seigo967--- via AMBER <
amber.ambermd.org<mailto:
amber.ambermd.org>> schrieb am Do., 19. Juni 2025, 07:18:
Dear All
I'm working on molecular dynamics simulation of membrane proteine using AMBER24.
I created a simulation system using packmol-memgen in AmberTools.
But protein wasn't pack into the centre of bilayer lipid membrane.
In addition, protein wasn't pack perpendicular to the xy plane.
(The molecular shape of my protein is highly anisotropic not like globular protein.)
How can I solve this problem?
The script for creation of the membrane system is shown below.
packmol-memgen --pdb mypdb.pdb --lipids POPC --ratio 1 --ffprot 'ff19SB' --ffwat 'opc' --fflip 'lipid21' --random --salt --leapline "loadAmberParams frcmod.ionslm_hfe_opc" --salt_c Na+ --salt_a Cl- --nloop 25 --parametrize
Thanks in advance.
Seigo Yumura
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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 - 00:30:01 PDT
