Dear Justin,<br><br>Thanks for your reply. Where is the error?<br><br>Pdb file:<br><br>ATOM 1 N ALA A 4<br>ATOM 2 CA ALA A 4<br>....<br>ATOM 2688 N ALA B 4<br>ATOM 2689 CA ALA B 4<br>....<br>
ATOM 5449 OXT GLN B 361<br>TER 5450 GLN B 361<br>HETATM 5451 OAAABSG A 1 <br>HETATM 5452 OABABSG A 1 <br>....<br>HETATM 5474 OAAABSG B 2<br>HETATM 5475 OABABSG B 2<br>....<br>HETATM 5492 O HOH A 2<br>
HETATM 5493 O HOH A 362<br>HETATM 5494 O HOH A 363<br>....<br>HETATM 5744 O HOH B 362<br>HETATM 5745 O HOH B 363<br><br><div class="gmail_quote">29 Aralık 2010 19:12 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Mark,<br>
<br>
The chain identifier have continuous. In sequence does not show any problem.<br>
<br>
<br>
</blockquote>
<br></div>
Then you're not looking at the right contents; pdb2gmx wouldn't complain otherwise. Usually HETATM entries like HOH (water) are after all protein chains, so you might have chains A, B, C, etc for protein followed by A, B, C, etc for water. Have a more thorough look through the .pdb file.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
29 Aralık 2010 15:10 tarihinde Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> yazdı:<div class="im">
<br>
<br>
On 29/12/2010 10:12 PM, ahmet yıldırım wrote:<br>
<br>
Dear users,<br>
<br>
ab@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p<br>
<br>
Select the Force Field:<br>
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
<br>
Fatal error:<br>
Chain identifier 'A' was used in two non-sequential blocks<br>
(residue 710, atom 54 49)<br>
<br>
What should I do to correct this error?<br>
<br>
<br>
Look at the entries whose chain identifier is A, and see why they<br>
are non-sequential, and take suitable action to remedy. You may need<br>
to Google for the PDB file format if you don't already understand it.<br>
<br>
Mark<br>
<br>
<br>
<br>
Thanks in advance<br>
<br>
-- Ahmet YILDIRIM<br>
<br>
<br>
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<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>