Hi Nahren,<br><br>Can you paste your actual command line where you used sed?<br><br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel <span dir="ltr"><<a href="mailto:meetnahren@yahoo.com">meetnahren@yahoo.com</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;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top">
Dear Gromacs Users,<br><br>thanks for all your suggestions. <br><br>Tsjerk, I did try your idea, but unfortunately doesn't seem to work.<br><br>the pdb file is shared here : <a href="http://www.4shared.com/account/file/ijofD83b/DIMER.html" target="_blank">http://www.4shared.com/account/file/ijofD83b/DIMER.html</a><br>
<br>newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh <br><br>Fatal error:<br>Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms<br>while sorting atoms.<br>.<br><br><br>Part of the file is pasted below:<br>
<br>ATOM 2836 N CYS R 283 -27.431 91.636 -6.099 1.00 0.00 N<br>ATOM 2837 H CYS R 283 -27.855 90.779 -6.392 1.00 0.00
H<br>ATOM 2838 CA CYS R 283 -26.033 91.780 -6.514 1.00 0.00 C<br>ATOM 2839 CB CYS R 283 -25.500 90.433 -7.060 1.00 0.00 C<br>ATOM 2840 SG CYS R 283 -25.121 89.114 -5.829 1.00 0.00 S<br>
ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 0.00 H<br>ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00 0.00
C<br>ATOM 2843 OXT CYS R 283 -26.993 93.593 -7.927 1.00 0.00 O<br>ATOM 2845 N LYS B 284 -23.431 108.789 63.478 1.00 0.00 N<br>ATOM 2846 H1 LYS B 284 -23.779 109.339 64.238 1.00 0.00 H<br>
ATOM 2847 H2 LYS B 284 -23.156 109.392 62.730 1.00 0.00 H<br><br><br>Best,<br>nahren<br><br>--- On <b>Tue, 9/7/10, Tsjerk Wassenaar <i><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></i></b> wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>><br>Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Date: Tuesday, September 7, 2010, 11:14 AM<br><br><div><div><div></div><div class="h5">
Hi,<br><br>> One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the fixed-column format correct) might be needed.<br>
<br>There should be only one OXT per chain. Removing those seems like a good idea:<br><br>sed -i '/^ATOM.*OXT/d' file.pdb<br>(Remove all lines starting with ATOM and containing OXT, in the file)<br><br>Hope it helps,<br>
<br>Tsjerk<br><br><br>--<br>Tsjerk A.
Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>Groningen Institute for Biomolecular Research and Biotechnology /<br>University of Groningen<br>The Netherlands<br></div></div>--<div class="im">
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Please don't post (un)subscribe requests to the list. Use the<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>
<br>post-doctoral researcher<br>Molecular Dynamics Group<br>Groningen Institute for Biomolecular Research and Biotechnology / <br>University of Groningen<br>The Netherlands<br>