[gmx-users] Error- Atom not found in residue seq nr while adding atom
jcb1 at um.es
Wed Apr 18 13:03:23 CEST 2012
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
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.
> 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.
> 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
Javier CEREZO BASTIDA
Universidad de Murcia
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