[gmx-users] Error- Atom not found in residue seq nr while adding atom

[Justin A. Lemkul]

aiswarya pawar wrote:
> 
> Hi Javier,
> 
> I did tried using the swisspdb for adding missing atoms still am 
> receiving the same error.
> 

The other possibility is that you have a naming mismatch.  In this case, pdb2gmx 
expects to find an atom named "ND1" in your residue but cannot.

-Justin

> 
> On Wed, Apr 18, 2012 at 3:44 PM, Javier Cerezo <jcb1 at um.es 
> <mailto:jcb1 at um.es>> wrote:
> 
>     Your PDB structure have probably some missing atoms. Check if this
>     is the case for residue nr. 7.
> 
>     To solve it you can use an external tool to process your PDB file
>     adding the missing atoms. I've used SwissPDB and worked fine.
> 
>     Javier
> 
>     El 18/04/12 11:24, aiswarya pawar escribió:
>>     Hi Users,
>>
>>     I did the following step=
>>      pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top
>>
>>
>>     and received an error= Atom ND1 not found in residue seq.nr
>>     <http://seq.nr>. 7 while adding atom.
>>
>>     I dont understand how do i rectify this.
>>
>>
>>     -- 
>>     Aiswarya
>>
>>
> 
>     -- 
>     Javier CEREZO BASTIDA
>     PhD Student
>     Physical Chemistry
>     Universidad de Murcia
>     Murcia (Spain)
>     Tel: (+34)868887434
> 
>     --
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> 
> 
> 
> -- 
> Aiswarya  B Pawar
> 
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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