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

From: David A Case <>
Date: Mon, 13 May 2019 09:50:41 -0400

On Mon, May 13, 2019, Maximilien BERNE wrote:
>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.

This isn't really an answer to you problem, but a couple of comments
from an outsider--I hope the lipid experts on this list will chime in with
corrections or suggestions:

1. Should the CHARMM-GUI not create Amber files itself? That is, what
is the need for charmmlipid2amber any more? (The lipid14 tutorial on
the web page is by now 5 years old....)

2. The AMBAT or packmol_memgen routines (the latter significantly
updated in AmberTools19, just released) provides alternative
Amber-centric methods for creating these systems. See Sections 12.6 and
12.7 in the Amber 2019 Reference Manual. That said, tutorials or
expanded explanations would be most helpful here.

3. Someone with lipid experience might try to answer the original


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Received on Mon May 13 2019 - 07:00:02 PDT
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