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What's residue nr. 7? Is it an standard one? <br>
<br>
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?<br>
<br>
Javier<br>
<br>
El 18/04/12 12:34, aiswarya pawar escribió:
<blockquote
cite="mid:CAEa6cRBb82mFLH_8vBFYaztdwP4TDTA0VROOWveE070kYNCF5Q@mail.gmail.com"
type="cite"><br>
Hi Javier,<br>
<br>
I did tried using the swisspdb for adding missing atoms still am
receiving the same error.<br>
<br>
<br>
<div class="gmail_quote">On Wed, Apr 18, 2012 at 3:44 PM, Javier
Cerezo <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jcb1@um.es">jcb1@um.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Your PDB structure have
probably some missing atoms. Check if this is the case for
residue nr. 7. <br>
<br>
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.<br>
<br>
Javier<br>
<br>
El 18/04/12 11:24, aiswarya pawar escribió:
<div>
<div class="h5">
<blockquote type="cite">Hi Users,<br>
<br>
I did the following step=<br>
pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top<br
clear="all">
<br>
<br>
and received an error= Atom ND1 not found in residue <a
moz-do-not-send="true" href="http://seq.nr"
target="_blank">seq.nr</a>. 7 while adding atom.<br>
<br>
I dont understand how do i rectify this.<br>
<br>
<br>
-- <br>
Aiswarya <br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
<span class="HOEnZb"><font color="#888888">
<div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: (+34)868887434 </div>
</font></span></div>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Aiswarya B Pawar<br>
<br>
<div>
Project Assistant,<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
<br>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: (+34)868887434
</div>
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