> Date: Mon, 30 Dec 2013 16:43:15 +0800
> From: YIPY0005.e.ntu.edu.sg
> To: amber.ambermd.org
> Subject: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages
>
> Hi,
>
> I built a protein structure via homology modeling, and there were some
> adjacent residues which I tried to use the "bond" command to link the C and
> N atoms so as to from amide linkages. However, I received the following
> error message:
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1773
> !FATAL: Message: 1-4: cannot add bond 1113 1115
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
This is due to, the connect records for your C - N bond are already present in PDB file. You can visualize that bond using xleap. So no need of bond command.
Or if you want to add them using bond command, just remove all the connect record's from the bottom of the PDB file.
Hope it helps
~Tumbi
> What can I do to resolve this problem?
>
> --
> Regards
> Yip Yew Mun
> Graduate, PhD
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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=-=-=-=
Tumbi Mohammad Khaled Abdul Waheed,
Research Scholar,
Department Of Pharmacoinformatics,
NIPER, S.A.S. Nagar, Mohali,
Punjab, India.Mob. +91 78145 24855
www.niper.gov.in
My Blog: http://pin4matics.wordpress.com
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Received on Mon Dec 30 2013 - 01:00:03 PST
