<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francesco,<div><span class="Apple-tab-span" style="white-space: pre; "> </span>Amber/Chimera expects the name of the hydrogen bonded to the backbone nitrogen in a negatively-charged cysteine to be HN (your structure has H). I have amended the code to allow H as well, so Chimera will handle your structure "correctly" in the next daily build.</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>I put quotes around correctly because are you really expecting all those cysteines to be negatively charged (i.e. not involved in a disulphide bond and no hydrogen on the sulfur)? Perhaps the CONECT records for the disulphide bonds weren't in the Reduce-generated PDB file? If that's the case you can rectify the problem by selecting all the cysteine sulfurs ("sel :cys@sg") and then running the Build Structure tool (its "Add/Delete Bonds" tab in your current build; "Adjust Bonds" tab in a newer build) to "Add reasonable bonds between selected atoms".</div><div><br></div><div>--Eric<div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><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 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 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><br></div></div></span></div></div></div><div><div>On Jun 10, 2010, at 11:55 AM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi:<br>With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein<br>with H atoms added with program REDUCE:<br><br>Tools -> Structure editing -> Dock prep (choice: If alternate<br>locations keep only the highest occupancy; Add charges; write mol2)<br>whereby I was asked to confirm residue CL- charge -1 and choose charge<br>method AM1-BCC.<br><br>getting warning: current charges are unknown for 1 non-standard atom<br>names in otherwise standard residues. Charge 0.0 assigned to unkknown<br>atoms. The log files reports:<br><br>Charge model: AMBER ff99SB<br>Assigning partial charges to residue CL- (net charge -1) with am1-bcc method<br>Non-standard atom names:<br> CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others)<br>Total charge for #0: -106.4198<br>The following residues had non-integral charges:<br> CYS 55.A -1.2719<br> CYS 134.A -1.2719<br> CYS 141.A -1.2719<br> CYS 156.A -1.2719<br> CYS 252.A -1.2719<br> CYS 272.A -1.2719<br> CYS 276.A -1.2719<br> CYS 285.A -1.2719<br> CYS 287.A -1.2719<br> CYS 299.A -1.2719<br> CYS 307.A -1.2719<br> CYS 323.A -1.2719<br> CYS 325.A -1.2719<br> CYS 329.A -1.2719<br> CYS 55.B -1.2719<br> CYS 134.B -1.2719<br> CYS 141.B -1.2719<br> CYS 156.B -1.2719<br> CYS 252.B -1.2719<br> CYS 272.B -1.2719<br> CYS 276.B -1.2719<br> CYS 285.B -1.2719<br> CYS 287.B -1.2719<br> CYS 299.B -1.2719<br> CYS 307.B -1.2719<br> CYS 323.B -1.2719<br> CYS 325.B -1.2719<br> CYS 329.B -1.2719<br> CYS 55.C -1.2719<br> CYS 134.C -1.2719<br> CYS 141.C -1.2719<br> CYS 156.C -1.2719<br> CYS 252.C -1.2719<br> CYS 272.C -1.2719<br> CYS 276.C -1.2719<br> CYS 285.C -1.2719<br> CYS 287.C -1.2719<br> CYS 299.C -1.2719<br> CYS 307.C -1.2719<br> CYS 323.C -1.2719<br> CYS 325.C -1.2719<br> CYS 329.C -1.2719<br><br>As an example, the mol2 file reads for CYS 55:<br><br>877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157<br> 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351<br> 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413<br> 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844<br> 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973<br> 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679<br> 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000<br> 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508<br> 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122<br> 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122<br>*****************************<br><br>In the past I encounterd a similar problem, solving it by adding atoms<br>with CHIMERA. This time, however, the complexity of the system<br>suggests to use REDUCE.<br><br>Thanks for suggestions.<br><br>francesco pietra<br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></body></html>