[gmx-users] Non Standard Residue in Amber

[Souvik Dey]

Hi,

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?

Regards,
Souvik

-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643