<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 14, 2010, at 1:22 PM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Eric:<br>Thanks. Headache adding hydrogen atoms (just as you mentioned addH)<br>with my present system. Neither CHIMERA nor REDUCE were able to treat<br>ASH/ASP HIP/HIE etc as I know from experiments, and software for pKa<br>simulation also dropped. But it may be my fault.<br></div></blockquote><div><br></div>As per the AddH documentation you should be able to get the protonation states you want if you specifically know those states beforehand:</div><div><br></div><div><h3 style="font-family: Times; "><a name="states">Protonation States</a></h3><p style="font-family: Times; "><b>AddH</b> aims to generate protonation states reasonable at physiological pH. For example, hydrogens are not added to the phosphodiester moieties of DNA and RNA. By default, aspartic acid and glutamic acid sidechains are assumed to be negatively charged, while arginine and lysine sidechains are assumed to be positively charged (although <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/addcharge/addcharge.html#alterstates">other states can be attained</a>). Two chemical moieties are treated as ambiguous at biological pH:</p><ul style="font-family: Times; "><li><font class="Apple-style-span" color="#8100FB">imidazoles such as histidine sidechains; histidine protonation states can be </font><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/addh/addh.html#hisprot"><font class="Apple-style-span" color="#8100FB">specified by the user</font></a> or guessed by the <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/addh/addh.html#method">method</a></li><li>terminal phosphates (the third ionization); if one P–O bond is at least 0.05 Å longer than the others around that same phosphorus atom, that oxygen will be protonated</li></ul><span class="Apple-style-span" style="font-family: Times; ">Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected as needed. For example, extra hydrogens can be</span><span class="Apple-style-span" style="font-family: Times; "> </span><span class="Apple-style-span" style="font-family: Times; "><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/editing.html#deletion">deleted</a></span><span class="Apple-style-span" style="font-family: Times; ">, and</span><span class="Apple-style-span" style="font-family: Times; "> </span><span class="Apple-style-span" style="font-family: Times; "><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html"><font class="Apple-style-span" color="#8100FB">atom types</font></a></span><span class="Apple-style-span" style="font-family: Times; "><font class="Apple-style-span" color="#8100FB"> </font></span><span class="Apple-style-span" style="font-family: Times; "><font class="Apple-style-span" color="#8100FB">can be edited (before hydrogen addition) with</font></span><span class="Apple-style-span" style="font-family: Times; "><font class="Apple-style-span" color="#8100FB"> </font></span><span class="Apple-style-span" style="font-family: Times; "><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html"><b><font class="Apple-style-span" color="#8100FB">setattr</font></b></a></span><span class="Apple-style-span" style="font-family: Times; "> </span><span class="Apple-style-span" style="font-family: Times; ">or</span><span class="Apple-style-span" style="font-family: Times; "> </span><span class="Apple-style-span" style="font-family: Times; "><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/editing.html"><b>Build Structure</b></a></span><span class="Apple-style-span" style="font-family: Times; ">.</span></div><div><br></div><div>That last part could probably use an example. Let's say you know that the asparagine which is residue 39 in chain A should have atom OD1 protonated. Changing the atom type to O3 (from O2-) [before AddH] would accomplish that:</div><div><br></div><div>setattr a idatmType O3 :39.a@od1</div><div><br></div><div>If you don't know specifically <i>which</i> oxygen should be protonated, this may not be a big help.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><blockquote type="cite"><div><br>As to the dockprep with either multiple pdb file, or single files<br>followed by "cat", it seems to me now that the latter is advantageous,<br>One can combine single-molecule mol2 files at will, and modify one or<br>more mol2 files without repeating the whole calculation.<br><br>francesco<br><br>On Mon, Jun 14, 2010 at 8:29 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<br><blockquote type="cite">On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">With the combined pdb file, does dockprep operate on single molecules<br></blockquote><blockquote type="cite">one after the other, so that it will not encounter obstacles even for<br></blockquote><blockquote type="cite">many (more complex) ligands?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I think this will be okay. Chimera ignores sibling submodels (e.g. #0.2 is<br></blockquote><blockquote type="cite">a "sibling" of #0.1) when adding hydrogens so you will be okay if all your<br></blockquote><blockquote type="cite">ligands come from one file.<br></blockquote><blockquote type="cite">--Eric<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Eric Pettersen<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> UCSF Computer Graphics Lab<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br></div></blockquote></div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><span class="Apple-style-span" style="font-size: medium;"><br class="Apple-interchange-newline"></span></div></span> </div><br></body></html>