well, either way, it's not up to specs... but we had bigger problems :)<br><br><div><span class="gmail_quote">On 2/3/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Tamas Horvath wrote:<br>> But... it's no big deal to change HEADER to REMARK, is it?
<br>According to the pdb standard HEADER is obligatory, which doesn't really<br>bother me in itself. However you can also do a one-liner<br><br>grep -v HEADER orig.pdb > new.pdb<br><br>to get rid of it...<br><br>><br>
> On 2/3/06, *Tamas Horvath* <<a href="mailto:hotafin@gmail.com">hotafin@gmail.com</a><br>> <mailto:<a href="mailto:hotafin@gmail.com">hotafin@gmail.com</a>>> wrote:<br>><br>> The BioJava PDB parser
<br>><br>><br>> On 2/3/06, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:
<br>><br>> Tamas Horvath wrote:<br>> > Hi!<br>> > trjconv generates an invalid HEADER record.<br>> ><br>> > REMARK GENERATED BY TRJCONV<br>> > HEADER Protein in water t=
0.00000<br>> > REMARK THIS IS A SIMULATION BOX<br>> ><br>> > According to the pdb file format specifications, it's an<br>> invalid header,<br>> > and it causes problems while parsing.
<br>> > So, can it be changed to REMARK?<br>> ><br>> > (Sorry if it has been changed since 3.2.1)<br>> ><br>> ><br>> ><br>> ------------------------------------------------------------------------
<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please don't post (un)subscribe requests to the list. Use the
<br>> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>>.<br>> > Can't post? Read<br>> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> <<a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a>><br>> What's wrong with it? The header should be a string of max 40<br>> characters, see<br>> <a href="http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html">
http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html</a><br>> <<a href="http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html">http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html
</a>><br>><br>> What software is complaining about it?<br>><br>> --<br>> David.<br>> ________________________________________________________________________<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755<br>>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><br>> <mailto:
<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a>> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> _______________________________________________
<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br>> <<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>><br>><br>><br>><br>><br>> ------------------------------------------------------------------------
<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>