Did you add the xml file to that directory and restart Analysis?

Wayne

On 21 Jul 2017, at 16:53, madhan kumar <[log in to unmask]> wrote:

Dear Wayne,

I am getting the following error message after I added NH2 at the end of the sequence.

Residue code(s) NH2 cannot be found for molecule type protein.

On Fri, Jul 21, 2017 at 9:02 PM, madhan kumar <[log in to unmask]> wrote:

Hi Wayne,

Thank so much. I will try as you mentioned and get back you.

Thanks,

Madhan Kumar

On Fri, Jul 21, 2017 at 8:55 PM, Wayne Boucher <[log in to unmask]> wrote:

Hello,

Fortunately Tim just passed through so he showed me how to create this NH2 as if it were an amino acid, so with the correct link to the “previous” residue.  So I’ve managed to create an NH2 xml ChemComp file of type “protein”, which I’ve attached.

Copy that file into your release directory into the subdirectory ccpnmr2.4/data/ccp/molecule/ChemComp/.  Then in the Molecule —> Molecules dialog go to the Add Sequence tab and in 3-letter/Ccp mode you can add NH2 at the end of your sequence.

Hopefully that will work.  (It seems to work for me but I haven’t gone much past the above.)

Wayne

On 21 Jul 2017, at 16:06, madhan kumar <[log in to unmask]> wrote:

Hi Brian, 

Yes. I did. My question is this: If my protein is having C terminal amidation, how can I add NH2 at the C  terminal when I am doing "Add Sequence".?

On Fri, Jul 21, 2017 at 4:56 PM, Brian Smith <[log in to unmask]> wrote:

Hi Madhan,

Have you tried copying your existing assignments to the new chain that you think you have created? If not give that a go first.

1. Archive your project!
2. follow:

https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/copy-assignments-between-molecular-chains

If this does not succeed, you haven't yet finished making your modified molecule - go back to

https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/create-a-sequence-with-unusual-amino-acids-or-nucleotides

Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
          College of Medical, Veterinary & Life Sciences,
  Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401

---

From: CcpNmr software mailing list [[log in to unmask]] on behalf of madhan kumar [[log in to unmask]]
Sent: 20 July 2017 14:21
To: [log in to unmask]
Subject: Assignment of C terminal amidated protein

Dear all,

I am using Analysis 2.4.2. I have a protein which is C-terminal amidated. I  did assignments for the protein without adding Nh2 at first in sequence. So I have created a new molsystem and new chain with the same sequence along with Nh2 at c terminal. I am having a problem to assign the Nh2 in 15N HSQC spectra. I picked the peak and gone for assignments. I did click assign but I couldn't see the newly added Molsystem at all. May I know how to do assignment for the same?

Thank you in advance.

--

Thanks & Regards,

M.Madhan Kumar,

Molecular Biophysics Unit,

Indian Institute of Science, 

Bangalore. India.

+91 8277200969

--

Thanks & Regards,

M.Madhan Kumar,

Molecular Biophysics Unit,

Indian Institute of Science, 

Bangalore. India.

+91 8277200969

--

Thanks & Regards,

M.Madhan Kumar,

Molecular Biophysics Unit,

Indian Institute of Science, 

Bangalore. India.

+91 8277200969

--

Thanks & Regards,

M.Madhan Kumar,

Molecular Biophysics Unit,

Indian Institute of Science, 

Bangalore. India.

+91 8277200969