<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Eric,<div class=""><br class=""></div><div class="">Following are steps I followed: load the structure> del H > run Dock Prep(Add Hydrogen - ticked, Write Mol2 - unticked) > del :10.P@h :8.T@h > minimize (<b class="">while deselecting the add hydrogen option</b>)</div><div class=""><br class=""></div><div class="">I got a warning that I am not sure about. I am pasting the log below[1], can you please confirm that I followed the correct steps and warning can be ignored in the log.</div><div class=""><br class=""></div><div class="">[1]</div><div class=""><div class=""><b class="">Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments.</b></div><div class=""><b class="">Automatically computing assignments using 'ksdssp' and parameter values:</b></div><div class=""><b class=""> energy cutoff -0.5</b></div><div class=""><b class=""> minimum helix length 3</b></div><div class=""><b class=""> minimum strand length 3</b></div><div class=""><b class="">Use command 'help ksdssp' for more information.</b></div><div class=""><b class="">Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments.</b></div><div class=""><b class="">Automatically computing assignments using 'ksdssp' and parameter values:</b></div><div class=""><b class=""> energy cutoff -0.5</b></div><div class=""><b class=""> minimum helix length 3</b></div><div class=""><b class=""> minimum strand length 3</b></div><div class=""><b class="">Use command 'help ksdssp' for more information.</b></div><div class=""><b class="">Residues with incomplete side chains:</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>LYS 98.A</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 100.A</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 218.A</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 824.A</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>GLU 50.C</b></div><div class=""><b class="">Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True'</b></div><div class=""><b class="">LYS 98.A: phi -78.3, psi 128.2 trans</b></div><div class=""><b class="">Chi angles for LYS 98.A:</b></div><div class=""><b class="">ASP 100.A: phi -70.1, psi -6.8 trans</b></div><div class=""><b class="">Chi angles for ASP 100.A:</b></div><div class=""><b class="">ASP 218.A: phi -127.8, psi 120.9 trans</b></div><div class=""><b class="">Chi angles for ASP 218.A:</b></div><div class=""><b class="">ASP 824.A: phi -92.0, psi 1.6 trans</b></div><div class=""><b class="">Chi angles for ASP 824.A:</b></div><div class=""><b class="">GLU 50.C: phi -60.9, psi -45.8 trans</b></div><div class=""><b class="">Chi angles for GLU 50.C:</b></div><div class=""><b class="">Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A</b></div><div class=""><b class="">Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A</b></div><div class=""><b class="">Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A</b></div><div class=""><b class="">Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C</b></div><div class=""><b class="">Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A</b></div><div class=""><b class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead</b></div><div class=""><b class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead</b></div><div class=""><b class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead</b></div><div class=""><b class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead</b></div><div class=""><b class="">Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T</b></div><div class=""><b class="">Chain-initial residues that are not actual N terminii: </b></div><div class=""><b class="">Chain-final residues that are actual C terminii: U 20.P, C 21.T</b></div><div class=""><b class="">Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C</b></div><div class=""><b class="">856 hydrogen bonds</b></div><div class=""><b class="">Removing spurious proton from 'C' of THR 929.A</b></div><div class=""><b class="">Removing spurious proton from 'C' of GLY 64.C</b></div><div class=""><b class="">Hydrogens added</b></div><div class=""><b class="">Charge model: AMBER ff14SB</b></div><div class=""><b class="">Non-standard atom names:</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>G H (G 10.P H)</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U H (U 8.T H)</b></div><div class=""><b class="">Total charge for #0: -30.384</b></div><div class=""><b class="">The following residues had non-integral charges:</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U 20.P -0.6919</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>C 21.T -0.6919</b></div><div class=""><font color="#0432ff" class=""><b class="">Correct charges are unknown for 2 non-standard atom names in otherwise standard residues</b></font></div><div class=""><font color="#0432ff" class=""><b class=""><br class=""></b></font></div><div class=""><font color="#0432ff" class=""><b class="">Charges of 0.0 were assigned to the unknown atoms</b></font></div><div class=""><font color="#0432ff" class=""><b class=""><br class=""></b></font></div><div class=""><font color="#0432ff" class=""><b class="">1 model(s) had non-integral total charge</b></font></div><div class=""><font color="#0432ff" class=""><b class="">Details in reply log</b></font></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">No incomplete side chains</b></div><div class=""><b class="">Charge model: AMBER ff14SB</b></div><div class=""><b class="">Total charge for #0: -30.384</b></div><div class=""><b class="">The following residues had non-integral charges:</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U 20.P -0.6919</b></div><div class=""><b class=""><span class="Apple-tab-span" style="white-space:pre"> </span>C 21.T -0.6919</b></div><div class=""><font color="#0432ff" class=""><b class="">1 model(s) had non-integral total charge</b></font></div><div class=""><font color="#0432ff" class=""><b class="">Details in reply log</b></font></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p</b></div><div class=""><b class="">Initial energy: -45283.236153 kJ/mol</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -58447.379716, Gradient norm: 758.031360</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.037342</b></div><div class=""><b class="">Finished 10 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -64213.179928, Gradient norm: 362.328469</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.018132</b></div><div class=""><b class="">Finished 20 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -65930.345155, Gradient norm: 417.614654</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.012606</b></div><div class=""><b class="">Finished 30 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -67901.748990, Gradient norm: 190.328174</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.010435</b></div><div class=""><b class="">Finished 40 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -68928.640793, Gradient norm: 79.670023</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.007430</b></div><div class=""><b class="">Finished 50 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -70504.551913, Gradient norm: 192.974949</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.016225</b></div><div class=""><b class="">Finished 60 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -71243.383589, Gradient norm: 95.907393</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.006255</b></div><div class=""><b class="">Finished 70 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -71661.708391, Gradient norm: 193.911209</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.006283</b></div><div class=""><b class="">Finished 80 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -72255.311758, Gradient norm: 199.037193</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.007288</b></div><div class=""><b class="">Finished 90 of 100 steepest descent minimization steps</b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -72873.927407, Gradient norm: 84.768251</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.005517</b></div><div class=""><b class="">Finished 100 of 100 steepest descent minimization steps</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">Step 12</b></div><div class=""><b class="">Potential energy: -79350.452189, Gradient norm: 206.369396</b></div><div class=""><b class="">Updated 15035 atoms. RMSD: 0.114423</b></div><div class=""><b class="">Finished 10 of 10 conjugate gradient minimization steps</b></div></div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">——<br class="">Jatin Kashyap <br class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div>
</div>
<div><br class=""><blockquote type="cite" class=""><div class="">On Sep 16, 2020, at 6:41 PM, <a href="mailto:chimera-users-request@cgl.ucsf.edu" class="">chimera-users-request@cgl.ucsf.edu</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Send Chimera-users mailing list submissions to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class="">or, via email, send a message with subject or body 'help' to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chimera-users-request@cgl.ucsf.edu<br class=""><br class="">You can reach the person managing the list at<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chimera-users-owner@cgl.ucsf.edu<br class=""><br class="">When replying, please edit your Subject line so it is more specific<br class="">than "Re: Contents of Chimera-users digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class=""> 1. Re: Error "No MMTK name for atom "H" in standard residue ?G""<br class=""> (Eric Pettersen)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Message: 1<br class="">Date: Wed, 16 Sep 2020 15:41:33 -0700<br class="">From: Eric Pettersen <pett@cgl.ucsf.edu><br class="">To: Jatin Kashyap <jk435@njit.edu><br class="">Cc: Chimera User Help <chimera-users@cgl.ucsf.edu><br class="">Subject: Re: [Chimera-users] Error "No MMTK name for atom "H" in<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>standard residue ?G""<br class="">Message-ID: <9B74E727-F918-4A68-9E48-83F05E6B329E@cgl.ucsf.edu><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">Ah I see. Because you also have missing side chains you have to do things a little differently. Namely run Dock Prep (Tools?Structure Editing?Dock Prep) first, keeping "Add hydrogens" on but "Write Mol2" off; then use the delete command to delete the two unwanted protons; then run Minimize.<br class=""><br class="">--Eric<br class=""><br class=""><blockquote type="cite" class="">On Sep 16, 2020, at 2:54 PM, Jatin Kashyap <jk435@njit.edu> wrote:<br class=""><br class="">I am sorry for the confusion. Actually I did that step by GUI options (Tools>Structure Editing>AddH). But I did it again by issuing ?addh? from command line along with other steps.<br class="">But still I am getting the same error.<br class=""><br class="">??<br class="">Jatin Kashyap <br class=""><br class=""><br class=""><blockquote type="cite" class="">On Sep 16, 2020, at 5:49 PM, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote:<br class=""><br class="">It's "addh" not "add H".<br class=""><br class="">--Eric<br class=""><br class=""><blockquote type="cite" class="">On Sep 16, 2020, at 2:44 PM, Jatin Kashyap <jk435@njit.edu <mailto:jk435@njit.edu>> wrote:<br class=""><br class="">Hi Eric,<br class=""><br class="">Just for the clarification I am double checking it here, first I loaded the structure > del H > add H > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option).<br class=""><br class="">But it is throwing the error [1].<br class=""><br class=""><br class="">[1]<br class="">Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments.<br class="">Automatically computing assignments using 'ksdssp' and parameter values:<br class=""> energy cutoff -0.5<br class=""> minimum helix length 3<br class=""> minimum strand length 3<br class="">Use command 'help ksdssp' for more information.<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead<br class="">Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T<br class="">Chain-initial residues that are not actual N terminii: <br class="">Chain-final residues that are actual C terminii: U 20.P, C 21.T<br class="">Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C<br class="">852 hydrogen bonds<br class="">Removing spurious proton from 'C' of THR 929.A<br class="">Removing spurious proton from 'C' of GLY 64.C<br class="">Hydrogens added<br class="">Residues with incomplete side chains:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>LYS 98.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 100.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 218.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 824.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>GLU 50.C<br class="">Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True'<br class="">LYS 98.A: phi -78.3, psi 128.2 trans<br class="">Chi angles for LYS 98.A:<br class="">ASP 100.A: phi -70.1, psi -6.8 trans<br class="">Chi angles for ASP 100.A:<br class="">ASP 218.A: phi -127.8, psi 120.9 trans<br class="">Chi angles for ASP 218.A:<br class="">ASP 824.A: phi -92.0, psi 1.6 trans<br class="">Chi angles for ASP 824.A:<br class="">GLU 50.C: phi -60.9, psi -45.8 trans<br class="">Chi angles for GLU 50.C:<br class="">Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A<br class="">Applying LYS rotamer (chi angles: -178.9 71.3 178.8 68.6) to LYS 98.A<br class="">Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A<br class="">Applying GLU rotamer (chi angles: -170.8 -83.2 25.9) to GLU 50.C<br class="">Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A<br class="">Charge model: AMBER ff14SB<br class="">Total charge for #0: -32.172<br class="">The following residues had non-integral charges:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>LYS 98.A -0.6068<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 100.A -1.0636<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 218.A -1.0636<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 824.A -1.0636<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>GLU 50.C -0.9909<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U 20.P -0.6919<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>C 21.T -0.6919<br class="">1 model(s) had non-integral total charge<br class="">Details in reply log<br class=""><br class="">Residue #0:98.A (LYS/lysine) is missing atoms H_gamma_3, H_epsilon_2, H_zeta_3, H_delta_2, H_epsilon_3, H_alpha, H_beta_3, H_gamma_2, H_delta_3, H_beta_2, H_zeta_1 and H_zeta_2 <br class=""><br class=""><br class="">??<br class="">Jatin Kashyap <br class=""><br class=""><br class=""><blockquote type="cite" class="">On Sep 16, 2020, at 5:32 PM, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote:<br class=""><br class="">Hi Jatin,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I you don't delete those phosphates, then Chimera will add spurious protons to them, which is what is causing the problem. In order to get this to work, you will have to run Add Hydrogens "by hand" before your minimization, delete the spurious protons, and then run your minimization -- being careful to skip adding hydrogens as part of the minimization process.<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The command (Favorites?Command Line) to delete the unwanted protons in your case is "del :10.P@h :8.T@h".<br class=""><br class="">--Eric<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Sep 16, 2020, at 2:10 PM, Jatin Kashyap <jk435@njit.edu <mailto:jk435@njit.edu>> wrote:<br class=""><br class="">Dear Chimera Community Members,<br class=""><br class="">I am facing an error while minimizing a protein that have 5? terminal phosphates attached to it. <br class="">Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. <br class="">I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2].<br class=""><br class="">Thank you for helping me to understand this.<br class=""><br class="">[1]<br class="">No MMTK name for atom "H" in standard residue ?G"<br class=""><br class="">[2]<br class="">Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments.<br class="">Automatically computing assignments using 'ksdssp' and parameter values:<br class=""> energy cutoff -0.5<br class=""> minimum helix length 3<br class=""> minimum strand length 3<br class="">Use command 'help ksdssp' for more information.<br class="">Residues with incomplete side chains:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>LYS 98.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 100.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 218.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ASP 824.A<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>GLU 50.C<br class="">Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True'<br class="">LYS 98.A: phi -78.3, psi 128.2 trans<br class="">Chi angles for LYS 98.A:<br class="">ASP 100.A: phi -70.1, psi -6.8 trans<br class="">Chi angles for ASP 100.A:<br class="">ASP 218.A: phi -127.8, psi 120.9 trans<br class="">Chi angles for ASP 218.A:<br class="">ASP 824.A: phi -92.0, psi 1.6 trans<br class="">Chi angles for ASP 824.A:<br class="">GLU 50.C: phi -60.9, psi -45.8 trans<br class="">Chi angles for GLU 50.C:<br class="">Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A<br class="">Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A<br class="">Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A<br class="">Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A<br class="">Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead<br class="">No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead<br class="">Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T<br class="">Chain-initial residues that are not actual N terminii: <br class="">Chain-final residues that are actual C terminii: U 20.P, C 21.T<br class="">Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C<br class="">856 hydrogen bonds<br class="">Removing spurious proton from 'C' of THR 929.A<br class="">Removing spurious proton from 'C' of GLY 64.C<br class="">Hydrogens added<br class="">Charge model: AMBER ff14SB<br class="">Non-standard atom names:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>G H (G 10.P H)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U H (U 8.T H)<br class="">Total charge for #0: -30.384<br class="">The following residues had non-integral charges:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>U 20.P -0.6919<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>C 21.T -0.6919<br class="">Correct charges are unknown for 2 non-standard atom names in otherwise standard residues<br class=""><br class="">Charges of 0.0 were assigned to the unknown atoms<br class=""><br class="">1 model(s) had non-integral total charge<br class="">Details in reply log<br class=""><br class="">No MMTK name for atom "H" in standard residue "G"<br class=""><br class=""><br class="">??<br class="">Jatin Kashyap <br class="">New Jersey Institute of Technology<br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu><br class="">Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users><br class=""></blockquote><br class=""></blockquote><br class="">_______________________________________________<br class="">Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu><br class="">Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users><br class=""></blockquote><br class=""></blockquote><br class=""></blockquote><br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200916/5eb743cc/attachment.html><br class=""><br class="">------------------------------<br class=""><br class="">Subject: Digest Footer<br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list<br class="">Chimera-users@cgl.ucsf.edu<br class="">Manage subscription:<br class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class=""><br class=""><br class="">------------------------------<br class=""><br class="">End of Chimera-users Digest, Vol 209, Issue 27<br class="">**********************************************<br class=""></div></div></blockquote></div><br class=""></div></body></html>