Hi,
Could you post the membrane PDB that you are loading into tleap? Or at least a small part of it, like the first 2-3 lipids. Also, your tleap command would be helpful.
Best,
Callum
-----Original Message-----
From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
Sent: Monday, May 13, 2019 8:42 AM
To: amber.ambermd.org
Subject: [AMBER] tleap split lipid when it shouldn't
Dear AMBERs,
i'm hoping you're having a nice day , and wish you could help someone in need.
So i try to make a MD on a protein with a lipid bilayer structure (created with CHARMM-GUI). my lipid is only with DOPC
using charmmlipid4amber, to create a file that will change my DOPC into OL and PC.
I succed to create the prmtop file and inpcrd . but after simulation i saw that my lipid are still split into three residues and that my bilayer structure is slowly looking like a sphere when the head of the lipid will just float around with water. I know that in force field lipid14 they split DOPC into those 3 residue.
but i would like to know if there is a way to maintain those residue together for my simulation.
i already tryed some things :
-scripting my files to recreate the bond between them, by deleting TER when it's need it (but then tleap will split them again) -rename my lipid in to OL , but then the ATOM (from PC) doesn't have a type in tleap
I join this with 2 images. First one from the lipid as it should be (linked together) , and the second one when load into tleap (then using savepdb to open it in chimera again) .
I'm greatfull that you spend some times helping me.
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Received on Mon May 13 2019 - 07:00:03 PDT
