[gmx-users] Non Standard Residue in Amber

[Mark Abraham]

Hi,

Probably all those tools work fine, but perhaps you haven't used them well.
Unfortunately we can't guess what errors you may have made without more
information...

Mark

On Wed, 26 Jul 2017 13:08 Souvik Dey <souvik.dey29 at gmail.com> wrote:

> 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
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