[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

On Wed, Jul 26, 2017 at 1:07 PM, 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
>



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