Re: [AMBER] tleap splitting the lipid

From: Matias Machado <>
Date: Mon, 08 Jun 2020 10:12:34 -0300 (UYT)

Dear Zhiyi Wu,

The issue and the solution is documented in this post:


Matias Machado

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Lunes, 8 de Junio 2020 9:22:36
Asunto: Re: [AMBER] tleap splitting the lipid

On Mon, Jun 08, 2020, zhiyi wu wrote:
>>>source leaprc.protein.ff14SB
>>>source leaprc.lipid17
>>>lipid = sequence {MY PC MY}
>>>savepdb lipid lipid.pdb
>However, I notice that instead of having a ter at the end of the
>molecule, there is a ter at the end of the first acryl chain (MY) another
>ter at the end of the head group (PC) and a final ter at the end of the

The simple workaround is to not use tleap to create the PDB file.
Instead, use ambpdb with the parm7 and rst7 files that tleap creates.
You can also use the writeCoordinates action in parmed. Both of these
examine the bond list to find where molecules begin and end.


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