Re: [AMBER] PIP2 lipids in Amber FF

From: Stephan Schott via AMBER <>
Date: Tue, 21 Jun 2022 18:57:54 +0200

Hi Ryan,

You should be able to generate a membrane with PIP2 using packmol-memgen,
though I have to warn you that I added parameters for them as a test for
myself. They haven't been validated thoroughly, so *use them at your own
risk. *With that said, in order to use them, you have to choose a proper
protonation state (I added a table for this in the manual), and you have to
parametrize your system with packmol-memgen to load the proper parameter
files (or at least, generate a suggestive tleap input, and keep it by using
"--keep"; you can modify this input file later on to adjust for frcmod
files and so on).

I am not sure why are you getting that error. Do you see something similar
for other python modules within amber? Parmed for example? How did you
compile/install amber? Which version are you using? Did you source the, or is you PYTHONPATH defined properly?

Best regards,

Stephan Schott Verdugo

Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf

El vie, 17 jun 2022 a las 22:39, Ryan Woltz via AMBER (<>)

> Dear Amber community,
> To the point: Is there a way to add in custom lipids into the Amber
> library? How do I build a system with lipids that are not compatible with
> CHARMM-GUI for Amber FF?
> Details
> I am a newcomer to Amber but have some experience using NAMD and
> GROMACS. I'm trying to build a protein complex embedded in a membrane with
> POPC and PIP2. I have done this using CHARMM-GUI and charmm36m FF but with
> these force fields things tend to expand between subunits. A Colleague
> suggested I use Amber as he does not see the same issues I'm having,
> although he is only using POPC. Unfortunately, my simulation requires PIP2
> (or SAPI24 in charmm36m FF). I found a list of compatible lipids for
> charmm-gui to build a lipid bilayer and it did not list any PI head groups.
> I found an old tutorial for Amber14 which says that Amber11 had PI head
> groups. I also looked at the Amber21lipid.lib on the amber lipid webpage
> and did not see any PI head group listed. I did not find anything about
> adding in custom lipids or how to build a system with custom lipids like
> you can for GROMACS and CG-MD. Any suggestions on whether this is possible?
> I'm not sure if this will help me but I've read about packmol-memgen
> but it is missing a module and I'm not quite sure how to fix that.
> packmol-memgen --help
> raceback (most recent call last):
> File "./packmol-memgen", line 4, in <module>
> from packmol_memgen.main import *
> No module named packmol_memgen.main
> If it is really complicated to generate a system in Amber FF with PIP2
> my alternative is just to use charmm36m FF and run in Amber (pmemd) and if
> need be put heavy weights on the 30+ atoms I'm worried about.
> Thank you and sorry if this is an already answered question, I did look
> around some but I'm new to Amber so not quite sure where all the resources
> are yet. I'm on ubuntu and Amber18.
> Ryan Woltz
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Received on Thu Aug 04 2022 - 13:32:55 PDT
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