[AMBER] LJEDIT syntax

From: Matias Machado <mmachado.pasteur.edu.uy>
Date: Mon, 23 Jul 2018 15:15:50 -0300 (UYT)

Dear AMBER experts,

I'm trying to set some Lennard-Jones interactions out-off the combination rule. I was able to do it by using Parmed, however I want to set them in a frcmod file so they can be applied by leap without further modification of the topology.

I know the LJEDIT section (available from amber14 on) would allow me to do so, however its syntax is poorly documented, indeed I couldn't find any mention to that keyword in the Amber manuals, nor in the file formats at the AMBER web page [http://ambermd.org/FileFormats.php]

The only reference I found was this post in the mailing list [http://dev-archive.ambermd.org/201301/0018.html], in which its implementation is discussed. From those comments, I would expect the following syntax:

LJEDIT
   <Type 1> <Type 2> <R* pair> <Eps pair>
   ...
END

However, looking at the implementation of parm14ipq.dat [https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
I found 4 terms instead of 2 for defining the LJ interaction, my guess is that 1-4 interactions can also be set separately but I'm not sure about that...

In any case... what does each set of parameters stand for?

Best regards,

Matías

------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[http://pasteur.uy/en/laboratorios-eng/lsbm]
[http://www.sirahff.com]

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Received on Mon Jul 23 2018 - 11:30:03 PDT
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