From: Sourav Ray (
Date: Fri May 29 2015 - 11:10:47 CDT

Hi Josh,

Someone suggested that and it worked fine! I never bothered to read the
topology and parameter files and hence was unaware of this quite useful
aspect of these files. I am using the automatic psf plugin and it works
fine now.

Caution: Anyone following this discussion please note using Molefacture to
amidate the protein made using Protein Builder is not a feasible and if so
a very tedious operation.


On Fri, May 29, 2015 at 9:26 PM, Josh Vermaas <> wrote:

> 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