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:

   <Type 1> <Type 2> <R* pair> <Eps pair>

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,


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

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