Hi Evan,
Nice to see someone trying this with charmm! I haven't updated the list of charmm lipids since I first started the script, so knowing someone is interested might just make me consider adding more functionalities in that direction.
The script should first look for pdb files in the current folder, i.e., L1.pdb and L2.pdb. Then you have to pass a custom memgen.parm file with information relevant for the packing with --memgen_parm, which should append (or replace if the same name is used) the info to the original list. You can just copy parameters for something that you deem similar in the included file. Of course this will not allow you to parametrize it with the script, but you should be able (maybe with some tweaking of the output pdb in between) to do it with psfgen afterwards. The rest of your command should work, just pay attention to protonation states, as by default the script trims and readds hydrogens with reduce.
Let me know if that sheds some light into it.
Cheers,
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),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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El mar, 7 may 2024 a la(s) 7:56 p.m., Evan Collins via AMBER (amber.ambermd.org<mailto:amber.ambermd.org>) escribió:
Hi Amber users,
I am interested in using the membrane builder for new ionizable lipids not currently standard in packmol-memgen.
Right now, I have generated .pdb and topology files (.prm, .itp) for each new ionizable lipid using CGENFF, and currently run self-assembly simulations in GROMACS with the CHARMM36 (July 2022) forcefield.
Alternatively, I am interested in trying prebuilt membranes and thus looked into packmol-memgen (AmberTools23). I am wondering how can I include lipids that aren’t already in memgen.param or pdbs.tar.gz?
Let’s say my new lipids are called “L1” and “L2”. What files would I need for L1 and L2; would a .pdb and .prm & .itp (for topology) suffice? How can I adjust memgen.param and/or other files to incorporate new lipid components into packmol-memgen? What would my ultimate command look like for membrane generation, something like this?
packmol-memgen --lipids L1:L2:POPC:CHL1 --ratio 1:1:1:1 --preoriented --salt --salt_c Na+ --saltcon 0.15 --dist 10 --dist_wat 15 –charmm
Any insight would be greatly appreciated.
Thanks,
Evan
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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),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 07 2024 - 12:30:02 PDT
