<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello,<div><br><div>I am new to gromacs. I am applying the pdb2gmx tool to a peptide that has an N-term pyroglutamate and a C-term amidation. The OPLS forcefield has an entry for PGLU.</div><div><br></div><div>I used the -ter flag of pdb2gmx to define protonation states of the termini. While this works fine for the C-term (choosing 3:None) I run into trouble with the PGLU at the N-term.</div><div><br></div><div>In my input pdb the nitrogen of PGLU is attached to CA, CD and one proton.</div><div><br></div><div>However when prompted 'Select start terminus type for PGLU-1' there is no NH option. If I select 'None' I get "Fatal error: There is a dangling bond at at least one of the terminal ends." If I chose NH2 I end up with too many protons at my N-terminus.</div><div><br></div><div>If I leave out the -ter flag altogether I get problems with my C-terminus: "Fatal error: atom C not found in building block 23NH2 while combining tdb and rtp".</div><div><br></div><div>How would I solve this?</div><div><br></div><div>Regards,</div><div><br></div><div>Henry</div><div><br></div><div><br></div><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></body></html>