<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Guys,<div><br></div><div>Thanks for past help received on this list.</div><div><br></div><div>I am having a problem which I hope I can get some insight on. I am trying to simulate Adenylate Kinase binding substrate analog AP5A (from Shapiro et al). The problem is that this ligand (which is basically two Adenosines chained together with five phosphates) is a little on the large side, with 68 atoms. I get the following error on trying to run genion: </div><div><br></div><div><div>Max #atoms in a charge group: 68 > 64</div><div><br></div><div>Can someone explain to me how the ligand is different from the protein (which certainly has more than 64 atoms!)? Is the protein not considered a charge group? Can I somehow tell gromacs not treat the ligand as something other than a charge group? Alternatively, can I increase the max # atoms in a charge group? I'm happy to let it run a little more slowly if that's the only consequence.</div><div><br></div><div>Many thanks</div><div><br></div></div><div>Sam</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-size: 12px; 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: 0; "><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-size: 12px; font-style: normal; font-variant: normal; 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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; "><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-size: 12px; 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; "><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-size: 12px; 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; "><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-size: 12px; 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; "><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-size: 12px; 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; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Samuel Coulbourn Flores</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Altman Lab</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Department of BioEngineering</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">Stanford University</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; "><a href="mailto:samuel.flores@aya.yale.edu">samuel.flores@aya.yale.edu</a></span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">650.644.8416</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; "><br class="webkit-block-placeholder"></span></font></div><div><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">花山</span></div><div><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">科学者</span></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">生物工学部</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">スタンフォ一ド大学</span></font></div><div><font class="Apple-style-span" face="'Hiragino Maru Gothic Pro'" size="4"><span class="Apple-style-span" style="font-size: 15px; white-space: pre-wrap; ">スタンフォ一ド、<span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; white-space: normal; "><span class="Apple-style-span" style="font-family: 'Hiragino Maru Gothic Pro'; font-size: 15px; white-space: pre-wrap; ">カリフォルニア、米国</span></span></span></font></div><div><br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>