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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:32:10 PDT
