<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thank you Tsjerk,<div><br><div><div>Now it works !</div><div><br></div><div>Cheers,</div><div><br></div><div>Henry<br><div><br><div><div><div>On 24 Nov 2011, at 23:11, Tsjerk Wassenaar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Henry,<br><br>Apparently NPCA is not listed as being protein, so pdb2gmx assumes<br>that the chain begins with GLY. Add NPCA to the file residuetypes.dat<br>one directory up, with the designation 'Protein'. I think that should<br>solve it.<br><br>Groetjes,<br><br>Tsjerk<br><br>On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking <<a href="mailto:H.G.Hocking@uu.nl">H.G.Hocking@uu.nl</a>> wrote:<br><blockquote type="cite">Thank you Tsjerk,<br></blockquote><blockquote type="cite">I am now trying with amber99.ff but have encountered the following problem:<br></blockquote><blockquote type="cite">My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp<br></blockquote><blockquote type="cite">and have updated aminoacids.r2b to include NPCA and I've even added an entry<br></blockquote><blockquote type="cite">in aminoacids.hdb for NPCA. Yet when I generate my itp/gro files using<br></blockquote><blockquote type="cite">pdb2gmx, the NPCA is recognises (all atoms are there) but the second residue<br></blockquote><blockquote type="cite">[ GLY ] is now changed to [ NGLY ] in the itp file despite still being the<br></blockquote><blockquote type="cite">second residue in the gro file. As a test, if I remove NGLY from<br></blockquote><blockquote type="cite">aminoacids.r2b it complains that 'there is no residue type for 'GLY' as a<br></blockquote><blockquote type="cite">starting terminus' thus ignoring that the first residue of my chain is in<br></blockquote><blockquote type="cite">fact NPCA.<br></blockquote><blockquote type="cite">What could be going on here? The -ter flag has no effect here as I noticed<br></blockquote><blockquote type="cite">that for all amber99XX.ff the aminoacids.n.tdb files are empty.<br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite">Henry<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Henry,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">That would be a bit of a wild west approach. A better approximation<br></blockquote><blockquote type="cite">would be taking the charges from the backbone amide group, as it is<br></blockquote><blockquote type="cite">just an amide with on either side aliphatic carbons. Doing it properly<br></blockquote><blockquote type="cite">is a bit more involved, as for the G53a6 FF you need to choose<br></blockquote><blockquote type="cite">parameters giving the right free enthalpy of solvation.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Groetjes,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Tsjerk<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking <<a href="mailto:H.G.Hocking@uu.nl">H.G.Hocking@uu.nl</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Dear all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">way I could adapt these to gromos53a6.ff?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Can I use, for example, the gromos53a6.ff atom types from glutamine,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">add/remove appropriate bonds / angles / impropers and then take the<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">that what I've just suggested is the cowboy method and that in reality it is<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">not that straightforward, right?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Kind regards,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Henry<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Henry Hocking, PhD<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Utrecht University<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Bijvoet Center for Biomolecular Research<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Padualaan 8<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">3584 CH Utrecht, The Netherlands<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Phone: +31-30-2532875<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Fax: +31-30-253 7623<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">E-mail: <a href="mailto:H.G.Hocking@uu.nl">H.G.Hocking@uu.nl</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Please search the archive at<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Tsjerk A. Wassenaar, Ph.D.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">post-doctoral researcher<br></blockquote><blockquote type="cite">Molecular Dynamics Group<br></blockquote><blockquote type="cite">* Groningen Institute for Biomolecular Research and Biotechnology<br></blockquote><blockquote type="cite">* Zernike Institute for Advanced Materials<br></blockquote><blockquote type="cite">University of Groningen<br></blockquote><blockquote type="cite">The Netherlands<br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at<br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--------------------------------------------------------<br></blockquote><blockquote type="cite">Henry Hocking, PhD<br></blockquote><blockquote type="cite">Utrecht University<br></blockquote><blockquote type="cite">Bijvoet Center for Biomolecular Research<br></blockquote><blockquote type="cite">Padualaan 8<br></blockquote><blockquote type="cite">3584 CH Utrecht, The Netherlands<br></blockquote><blockquote type="cite">Phone: +31-30-2532875<br></blockquote><blockquote type="cite">Fax: +31-30-253 7623<br></blockquote><blockquote type="cite">E-mail: <a href="mailto:H.G.Hocking@uu.nl">H.G.Hocking@uu.nl</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at<br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote><blockquote type="cite"><br></blockquote><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>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><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 <br>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 apple-content-edited="true"> <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: 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; "><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><span class="Apple-style-span" style="color: rgb(128, 128, 128); font-size: 12px; ">Henry Hocking, PhD</span></div><div><span class="Apple-style-span" style="color: rgb(128, 128, 128); font-size: 12px; "><br></span></div><div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">Utrecht University </font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">Bijvoet Center for Biomolecular Research</font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">Padualaan 8</font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">3584 CH Utrecht, The Netherlands</font></div></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080"><br></font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">Phone: +31-30-2532875</font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">Fax: +31-30-253 7623</font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#808080">E-mail: <a href="mailto:H.G.Hocking@uu.nl">H.G.Hocking@uu.nl</a></font></div><div><br></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></div></div></div></div></div></body></html>