[AMBER] tleap split lipid when it shouldn't

From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
Date: Mon, 13 May 2019 14:41:42 +0200 (CEST)

Dear AMBERs,

i'm hoping you're having a nice day , and wish you could help someone in

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.

AMBER mailing list

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Received on Mon May 13 2019 - 06:00:04 PDT
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