<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">This issue has been resolved so the next official release of gromacs will be capacle of using the newer versions of dssp.<div><br></div><div>Erik</div><div><br><div><div>14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Wow, just did that.<br>In Debian have to use 4.5.5-2 version of Gromacs from sid repository.<br>Still have to use the oldest dssp<br><a href="http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi">http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi</a><br><br>It was simply Gromacs issue with no ways around.<br> And it woks:)<br><br>Just wondering,<br> What are other efficient ways of analyzing secondary structure instead of dssp? (novice question)<br>Good luck to everybody<br><br><br>On 14.06.2012 11:59, Denis Kazakiewicz wrote:<br><blockquote type="cite">Hello<br></blockquote><blockquote type="cite">Dear Gromacs users.<br></blockquote><blockquote type="cite">This is many times discussed issue, however nothing seems to work so far<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">do_dssp returns "Segmentation fault"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It is the oldest version of dssp: dsspcmbi<br></blockquote><blockquote type="cite">Gromacs 4.5.5 on Debian i386<br></blockquote><blockquote type="cite">I did use export DSSP=/path to dssp<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">1. What is possibly could be?<br></blockquote><blockquote type="cite">2. Any other efficient ways of analyzing secondary structure without do_dssp (with VMD, may be)?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">THANKS in advance<br></blockquote><br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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