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,
MatÃas
------------------------------------
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
