<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="">Dear Chimera Community Members,<div class=""><br class=""></div><div class="">I am facing an error while minimizing a protein that have 5’ terminal phosphates attached to it. </div><div 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. </div><div 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].</div><div class=""><br class=""></div><div class="">Thank you for helping me to understand this.</div><div class=""><br class=""></div><div class="">[1]</div><div class=""><b class="">No MMTK name for atom "H" in standard residue “G"</b></div><div class=""><br class=""></div><div class="">[2]</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="">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: -175.9 -11.3) to ASP 218.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="">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=""><b class="">Correct charges are unknown for 2 non-standard atom names in otherwise standard residues</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">Charges of 0.0 were assigned to the unknown atoms</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">1 model(s) had non-integral total charge</b></div><div class=""><b class="">Details in reply log</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">No MMTK name for atom "H" in standard residue "G"</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="">New Jersey Institute of Technology</div></div></div></div></div></div></div></div></div></div></div></div></div>
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