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 <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
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========================================
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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