Hi,
Thanks for the prompt reply. However, the PDB which I loaded into tleap already had the connect records removed. Is it possible these records remain hidden after removal? Nonetheless, when I desc those atoms, tleap states that there is a single bond present.
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 30 Dec, 2013, at 4:54 pm, Mohammed Khaled Tumbi <khaledtumbi.outlook.com> wrote:
>> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> =-=-=-=
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 30 2013 - 01:30:03 PST
