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

[Javier Cerezo]

What's residue nr. 7? Is it an standard one?

The way to solve the problem is to inspect the PDB file where gmx2pdb 
encounters problems. In your case, take a look to residue nr. 7 and 
compare it with the residue specifications in the rtp file. Can you post 
both?

Javier

El 18/04/12 12:34, aiswarya pawar escribió:
>
> Hi Javier,
>
> I did tried using the swisspdb for adding missing atoms still am 
> receiving the same error.
>
>
> 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
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- 
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120418/91f1f632/attachment.html>