[AMBER] How can I pack a protein (not GPCR) into the centre of bilayer membrane and perpendicular to the xy plane?

From: yumura.seigo967--- via AMBER <amber.ambermd.org>
Date: Thu, 19 Jun 2025 05:15:01 +0000

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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Received on Wed Jun 18 2025 - 22:30:02 PDT