Itamar, thank you for advise but I dont like swith prot :))<br><br>Justin, what xleap prameter set have you used for KALP peptide? I want to find parameters wich would not affect any problems in my further simulation via gromos in Gromacs.<br>
<br><br>James<br><br><br><br><div class="gmail_quote">2011/10/31 Itamar Kass <span dir="ltr"><<a href="mailto:itamar.kass@monash.edu">itamar.kass@monash.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div style="word-wrap: break-word;">Hi James,<div><br></div><div>I usually use Swiss-PdbViewer (<a href="http://spdbv.vital-it.ch/disclaim.html" target="_blank">http://spdbv.vital-it.ch/disclaim.html</a>). Despite being an old and not well supported for any system, it is still a free and easy to use and allows the building and mutating of residues in addition to automatically adding missing atoms. </div>
<div><br></div><div>You can just build an extra GLY at the end of the your chain and using text editor change it to N/C-caps.</div><div><br></div><div><br></div><div>Cheers,</div><div>Itamar</div><div><br></div><div><div>
<div></div><div class="h5"><div><div>On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote:</div><br><blockquote type="cite"><div><blockquote type="cite">Dear Gromacs Users!<br></blockquote><blockquote type="cite"><br></blockquote>
<blockquote type="cite"><br></blockquote><blockquote type="cite">I'd like to know about external software wich could be used for structure<br></blockquote><blockquote type="cite">processing for the futher simulation in Gromacs. Today I've tried one of the<br>
</blockquote><blockquote type="cite">most popular such software Amber tools but I've forced with problems during<br></blockquote><blockquote type="cite">compilation of it ") So I'm looking for possible analogues )<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">First of all I'm intresting in software for the addition different CAPing<br></blockquote><blockquote type="cite">groups to N and C termi of my protein.<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is there any plugins for Pymol or VMD for such purposes? I've loked for this<br></blockquote><blockquote type="cite">option in both of that software but couldnot find<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you for your help,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">
James<br></blockquote><br>Among free solutions... maybe this would help:<br><a href="http://www.chemaxon.com/marvin/sketch/index.php" target="_blank">http://www.chemaxon.com/marvin/sketch/index.php</a><br><br>I don't know molecular editor plugins for VMD, but it would be cool,<br>
if one is accessible.<br><br>-- <br>Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.<br>Univ. Rochester, Rochester, New York 14627-0216<br>THE UNITED STATES OF AMERICA<br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</div></blockquote></div><br></div></div><div>
<div>-- </div><div><br></div><div>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut</div><div><br></div><div>===========================================</div>
<div>| Itamar Kass, Ph.D.</div><div>| Postdoctoral Research Fellow</div><div>|</div><div>| Department of Biochemistry and Molecular Biology</div><div>| Building 77 Clayton Campus</div><div>| Wellington Road</div><div>| Monash University,</div>
<div>| Victoria 3800</div><div>| Australia</div><div>|</div><div>| Tel: +61 3 9902 9376</div><div>| Fax: +61 3 9902 9500</div><div>| E-mail: <a href="mailto:Itamar.Kass@monash.edu" target="_blank">Itamar.Kass@monash.edu</a></div>
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