Re: [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 <j...@um.es 
<mailto:j...@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





--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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