This is very interesting, thanks Stephan. I’ll check it out.
Best,
Derek
Derek M. Shore, Ph.D.
Lecturer of Physiology and Biophysics
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu<mailto:des2037.med.cornell.edu>
From: Stephan Schott <s.schott-verdugo.fz-juelich.de>
Date: Thursday, March 14, 2024 at 6:39 PM
To: Derek M Shore <des2037.med.cornell.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: [EXTERNAL] Re: [AMBER] Amber FF simulations with lipids not in LIPID21
Hi Derek, I added some preliminary parameters for PIs in packmol-memgen. Check the manual for that. Best regards, Stephan Schott Verdugo Biochemist Computational Biophysical Chemistry Institut für Bio- und Geowissenschaften / Bioinformatik
Hi Derek,
I added some preliminary parameters for PIs in packmol-memgen. Check the manual for that.
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),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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El jue, 14 mar 2024 a la(s) 11:19 p.m., Derek M Shore via AMBER (amber.ambermd.org<mailto:amber.ambermd.org>) escribió:
Hi Amber community,
As described in the Amber manual, and here: https://ambermd.org/AmberModels_lipids.php<https://urldefense.com/v3/__https:/ambermd.org/AmberModels_lipids.php__;!!Aer6R9v1Nk4!9QXPlPTg3vtPP63l3__doBfI23RPLsp-MD6AjSaAplGH3qaEbIhXQbOStsYerDW44cmQBtpGHL8ji1VdZXnkikq7uZ2iwh9K84ukg7n-OQ$>, many types of lipids can be constructed from combinations of available head groups and acyl chains, in LIPID21.
However, is it possible to run lipid simulations (Amber FF) that are not one of the available combinations? For example, I’d like to be able to run simulations with phosphatidylinositol 4,5-bisphosphate (
https://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate<
https://urldefense.com/v3/__https:/en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate__;!!Aer6R9v1Nk4!9QXPlPTg3vtPP63l3__doBfI23RPLsp-MD6AjSaAplGH3qaEbIhXQbOStsYerDW44cmQBtpGHL8ji1VdZXnkikq7uZ2iwh9K84srUgW9dw$>), which sadly can’t be constructed from the available LIPID21 fragments.
Any advice about how one should approach this (or if it is even advisable) would be greatly appreciated.
Thanks,
Derek
Derek M. Shore, Ph.D.
Lecturer of Physiology and Biophysics
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu<mailto:
des2037.med.cornell.edu><mailto:
des2037.med.cornell.edu<mailto:
des2037.med.cornell.edu>>
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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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Received on Thu Mar 14 2024 - 17:00:02 PDT
