Just a follow up...
If you don't want to mess things up by manually editing the libraries, then you can do everything from LEAP's command line!
To do it you just have to define the "connect0" and "connect1" records of the residues... of course you will have to do this every time you set a new topology...
# Example
source leaprc.protein.ff14SB
source leaprc.lipid17
set MY.1 connect0 MY.1.C12
set MY.1 connect1 MY.1.C12
set PC.1 connect0 PC.1.C11
set PC.1 connect1 PC.1.C21
lipid = sequence {MY PC MY}
savepdb lipid lipid.pdb
# Done!
Best,
Matias
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 8 de Junio 2020 10:12:34
Asunto: Re: [AMBER] tleap splitting the lipid
Dear Zhiyi Wu,
The issue and the solution is documented in this post:
http://archive.ambermd.org/202001/0172.html
Best,
Matias Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "David A Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
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
>molecular.
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.
....dac
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Received on Mon Jun 08 2020 - 09:00:03 PDT
