[gmx-users] Non Standard Residue in Amber

Souvik Dey souvik.dey29 at gmail.com
Wed Jul 26 13:08:17 CEST 2017


I have a non standard residue, FAD, Flavin Adenine Dinucleotide. I need to
standardize it for running a simulation using Amber force field. I tried
ACPYPE but it is not working for this particular residue. I also read that
Parmed can be used for the same purpose, but I could not find how to use
it. Also, whenever, I am trying to run Gaussian with FAD, it comes with a
convergence error.

So, can anyone tell me how do I sort out this issue?


Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
West Bengal

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