VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri May 29 2015 - 10:56:45 CDT

Hi Sourav,

How do you normally generate your psf? In psfgen, the protein segment
would be patched with a non-default patch (CT2 from top_all36_prot.rtf),
resulting in amidation. You will need to provide more details as to how
you generate your psf... If its a tcl script, its easy to change.

-Josh Vermaas

On 05/28/2015 05:13 AM, Sourav Ray wrote:
> Hello
>
> I would like to carry out amidation (-NH2 addition) of carboxyl end of
> peptide and generate corresponding pdb and psf files. Can anyone help
> me with the steps to be followed, I read the tutorial but was not able
> to proceed.
>
> Regards
> Sourav