Re: [AMBER] tleap split lipid when it shouldn't

From: Maximilien BERNE <>
Date: Mon, 13 May 2019 16:32:03 +0200 (CEST)

thanks for your time here's the step
after creating my lipid with CHARMM-GUI i obtain this file (i recreate all
the step with only 2 lipid) :

#then in terminal i use ( i use AMBER16 )
$AMBERHOME/bin/ -i step5_assembly.pdb -o lip_amber.pdb

#using pdb4amber to use it in tleap lip_amber.pdb => lip_amber_reduce.pdb

$AMBERHOME/bin/pdb4amber -i lip_amber.pdb --dry --nohyd --reduce
--add-missing-atoms -o lip_amber_reduce.pdb -l

#then i load it in tleap


> 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 <>
> Sent: Monday, May 13, 2019 8:42 AM
> To:
> 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 - 08:00:01 PDT
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