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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Eric </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Problems with atom names in adding charge to a receptor using Chimera v1.13.1
</p>
<p class="MsoNormal">(Tools<span style="font-family:Wingdings">à</span>Surface Binding/Analysis<span style="font-family:Wingdings">à</span>Add charge)</p>
<p class="MsoNormal">I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF.</p>
<p class="MsoNormal">Net Charge is +0 for the residue HIS using charge method AM1_BCC</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Chimera warning received</p>
<p class="MsoNormal">Correct charges are unknown for 9 non-standard atom names in otherwise standard residues.</p>
<p class="MsoNormal">Charges of 0.0 were assigned to the unknown atoms.</p>
<p class="MsoNormal">1 model(s) had non-intergral total charge.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Reply log is as follows,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Charge model: AMBER ff14SB</p>
<p class="MsoNormal">Assigning partial charges to residue HIS (net charge +0) with am1-bcc method</p>
<p class="MsoNormal">Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2 -fi mol2 -o c:\users\hp\appdata\local\temp\tmplj8p6o\ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n</p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Welcome to antechamber 17.3: molecular input file processor.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2).</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Info: Total number of electrons: 78; net charge: 0</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/BCCPARM.DAT" -s 2 -j 1</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(HIS) </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Charges for residue HIS determined</p>
<p class="MsoNormal">Non-standard atom names:</p>
<p class="MsoNormal"> VAL HB1 (VAL 551.A HB1)</p>
<p class="MsoNormal"> VAL HB2 (VAL 551.A HB2)</p>
<p class="MsoNormal"> ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3)</p>
<p class="MsoNormal"> VAL HB3 (VAL 551.A HB3)</p>
<p class="MsoNormal"> ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2)</p>
<p class="MsoNormal"> THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1)</p>
<p class="MsoNormal"> ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1)</p>
<p class="MsoNormal"> THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3)</p>
<p class="MsoNormal"> THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2)</p>
<p class="MsoNormal">Total charge for #0: -66.402</p>
<p class="MsoNormal">The following residues had non-integral charges:</p>
<p class="MsoNormal"> LYS 16.A 0.0867</p>
<p class="MsoNormal"> LEU 27.A -0.0471</p>
<p class="MsoNormal"> GLN 29.A 0.0392</p>
<p class="MsoNormal"> LYS 37.A 0.0867</p>
<p class="MsoNormal"> LYS 47.A 0.0733</p>
<p class="MsoNormal"> ASP 52.A -0.2088</p>
<p class="MsoNormal"> GLU 53.A -0.2103</p>
<p class="MsoNormal"> GLU 56.A -0.1137</p>
<p class="MsoNormal"> LYS 69.A 0.0867</p>
<p class="MsoNormal"> ARG 77.A 0.0612</p>
<p class="MsoNormal"> GLU 78.A -0.1137</p>
<p class="MsoNormal"> THR 79.A 0.3128</p>
<p class="MsoNormal"> TYR 80.A 0.0451</p>
<p class="MsoNormal"> GLU 82.A -0.1137</p>
<p class="MsoNormal"> GLN 90.A 0.0152</p>
<p class="MsoNormal"> GLU 91.A -0.1137</p>
<p class="MsoNormal"> GLU 93.A -0.1137</p>
<p class="MsoNormal"> ARG 94.A 0.0612</p>
<p class="MsoNormal"> PHE 98.A 0.0352</p>
<p class="MsoNormal"> GLN 100.A 0.0392</p>
<p class="MsoNormal"> ASN 107.A 0.0397</p>
<p class="MsoNormal"> ARG 110.A 0.0612</p>
<p class="MsoNormal"> LYS 132.A 0.0867</p>
<p class="MsoNormal"> LYS 133.A 0.2148</p>
<p class="MsoNormal"> LYS 155.A 0.0867</p>
<p class="MsoNormal"> LYS 158.A 0.0733</p>
<p class="MsoNormal"> GLN 166.A 0.0152</p>
<p class="MsoNormal"> LYS 170.A 0.0733</p>
<p class="MsoNormal"> LEU 174.A -0.0471</p>
<p class="MsoNormal"> LYS 186.A 0.0867</p>
<p class="MsoNormal"> GLN 200.A 0.0152</p>
<p class="MsoNormal"> LYS 201.A 0.0733</p>
<p class="MsoNormal"> ARG 205.A 0.153</p>
<p class="MsoNormal"> LYS 221.A 0.0867</p>
<p class="MsoNormal"> LYS 229.A 0.0733</p>
<p class="MsoNormal"> LYS 236.A 0.0733</p>
<p class="MsoNormal"> LEU 247.A -0.0471</p>
<p class="MsoNormal"> LYS 272.A 0.0733</p>
<p class="MsoNormal"> GLU 273.A -0.1137</p>
<p class="MsoNormal"> GLU 276.A -0.1137</p>
<p class="MsoNormal"> LYS 277.A 0.0733</p>
<p class="MsoNormal"> GLU 281.A -0.1137</p>
<p class="MsoNormal"> LYS 282.A 0.0733</p>
<p class="MsoNormal"> GLU 293.A -0.1137</p>
<p class="MsoNormal"> LEU 298.A -0.0471</p>
<p class="MsoNormal"> LYS 309.A 0.0733</p>
<p class="MsoNormal"> LYS 319.A 0.0867</p>
<p class="MsoNormal"> ASP 320.A -0.2088</p>
<p class="MsoNormal"> LYS 355.A 0.0867</p>
<p class="MsoNormal"> ASP 361.A -0.2088</p>
<p class="MsoNormal"> LYS 368.A 0.0867</p>
<p class="MsoNormal"> LYS 374.A 0.0733</p>
<p class="MsoNormal"> GLU 378.A -0.1137</p>
<p class="MsoNormal"> GLU 392.A -0.1137</p>
<p class="MsoNormal"> GLN 393.A 0.0152</p>
<p class="MsoNormal"> LYS 398.A 0.0733</p>
<p class="MsoNormal"> LEU 404.A -0.0471</p>
<p class="MsoNormal"> LYS 428.A 0.0867</p>
<p class="MsoNormal"> LYS 432.A 0.0867</p>
<p class="MsoNormal"> LYS 462.A 0.0733</p>
<p class="MsoNormal"> LYS 496.A 0.0867</p>
<p class="MsoNormal"> GLU 497.A -0.2103</p>
<p class="MsoNormal"> ASN 499.A 0.0397</p>
<p class="MsoNormal"> ILE 509.A 0.0431</p>
<p class="MsoNormal"> LYS 515.A 0.0733</p>
<p class="MsoNormal"> GLU 516.A -0.1137</p>
<p class="MsoNormal"> LYS 520.A 0.0733</p>
<p class="MsoNormal"> LEU 528.A -0.0471</p>
<p class="MsoNormal"> LYS 532.A 0.0733</p>
<p class="MsoNormal"> LYS 534.A 0.0733</p>
<p class="MsoNormal"> LYS 537.A 0.0733</p>
<p class="MsoNormal"> LYS 541.A 0.0733</p>
<p class="MsoNormal"> PHE 547.A 0.0352</p>
<p class="MsoNormal"> VAL 551.A 0.1935</p>
<p class="MsoNormal"> LYS 553.A 0.2148</p>
<p class="MsoNormal"> LYS 556.A 0.0733</p>
<p class="MsoNormal"> ASP 558.A -0.2088</p>
<p class="MsoNormal"> LYS 560.A 0.0733</p>
<p class="MsoNormal"> GLU 561.A -0.1137</p>
<p class="MsoNormal"> GLU 566.A -0.2103</p>
<p class="MsoNormal"> LYS 569.A 0.0733</p>
<p class="MsoNormal"> LYS 570.A 0.0733</p>
<p class="MsoNormal"> GLN 576.A 0.0152</p>
<p class="MsoNormal"> LYS 586.B 0.0733</p>
<p class="MsoNormal"> LEU 605.B -0.0471</p>
<p class="MsoNormal"> GLN 606.B 0.0152</p>
<p class="MsoNormal"> THR 621.B 0.3128</p>
<p class="MsoNormal"> LYS 625.B 0.0733</p>
<p class="MsoNormal"> ASP 630.B -0.2088</p>
<p class="MsoNormal"> GLU 634.B -0.1137</p>
<p class="MsoNormal"> ASN 635.B 0.0397</p>
<p class="MsoNormal"> LYS 638.B 0.0867</p>
<p class="MsoNormal"> GLU 656.B -0.1137</p>
<p class="MsoNormal"> THR 657.B 0.3128</p>
<p class="MsoNormal"> TYR 658.B 0.0451</p>
<p class="MsoNormal"> GLU 660.B -0.1137</p>
<p class="MsoNormal"> MET 661.B 0.0564</p>
<p class="MsoNormal"> LYS 667.B 0.0733</p>
<p class="MsoNormal"> GLN 668.B 0.0152</p>
<p class="MsoNormal"> GLU 671.B -0.1137</p>
<p class="MsoNormal"> ARG 672.B 0.0612</p>
<p class="MsoNormal"> PHE 676.B 0.0352</p>
<p class="MsoNormal"> GLN 678.B 0.0152</p>
<p class="MsoNormal"> ARG 688.B 0.0612</p>
<p class="MsoNormal"> LEU 689.B -0.0471</p>
<p class="MsoNormal"> LYS 733.B 0.0733</p>
<p class="MsoNormal"> GLN 744.B 0.0152</p>
<p class="MsoNormal"> LYS 748.B 0.0733</p>
<p class="MsoNormal"> LEU 752.B -0.0471</p>
<p class="MsoNormal"> LYS 755.B 0.0733</p>
<p class="MsoNormal"> ARG 760.B 0.0612</p>
<p class="MsoNormal"> GLU 762.B -0.1137</p>
<p class="MsoNormal"> LYS 764.B 0.2148</p>
<p class="MsoNormal"> GLN 778.B 0.0152</p>
<p class="MsoNormal"> LYS 779.B 0.0867</p>
<p class="MsoNormal"> ARG 783.B 0.3792</p>
<p class="MsoNormal"> LYS 799.B 0.0867</p>
<p class="MsoNormal"> LYS 807.B 0.0733</p>
<p class="MsoNormal"> LYS 814.B 0.0733</p>
<p class="MsoNormal"> LEU 849.B -0.0471</p>
<p class="MsoNormal"> LYS 850.B 0.0733</p>
<p class="MsoNormal"> GLU 851.B -0.1137</p>
<p class="MsoNormal"> GLU 854.B -0.1137</p>
<p class="MsoNormal"> LYS 855.B 0.0867</p>
<p class="MsoNormal"> LYS 860.B 0.0733</p>
<p class="MsoNormal"> GLU 871.B -0.1137</p>
<p class="MsoNormal"> ASP 875.B -0.2088</p>
<p class="MsoNormal"> LYS 887.B 0.0733</p>
<p class="MsoNormal"> LYS 891.B 0.0733</p>
<p class="MsoNormal"> GLU 895.B -0.1137</p>
<p class="MsoNormal"> LYS 897.B 0.0867</p>
<p class="MsoNormal"> LYS 933.B 0.2148</p>
<p class="MsoNormal"> GLU 942.B -0.1137</p>
<p class="MsoNormal"> LYS 952.B 0.0867</p>
<p class="MsoNormal"> GLU 956.B -0.1137</p>
<p class="MsoNormal"> LYS 963.B 0.2148</p>
<p class="MsoNormal"> LYS 976.B 0.0867</p>
<p class="MsoNormal"> ARG 984.B 0.3792</p>
<p class="MsoNormal"> LYS 1010.B 0.0867</p>
<p class="MsoNormal"> LYS 1018.B 0.2148</p>
<p class="MsoNormal"> LYS 1040.B 0.0733</p>
<p class="MsoNormal"> GLU 1075.B -0.1137</p>
<p class="MsoNormal"> ASP 1086.B -0.2088</p>
<p class="MsoNormal"> ILE 1087.B 0.0431</p>
<p class="MsoNormal"> LYS 1093.B 0.0733</p>
<p class="MsoNormal"> GLU 1094.B -0.1137</p>
<p class="MsoNormal"> GLN 1096.B 0.0152</p>
<p class="MsoNormal"> LYS 1098.B 0.0867</p>
<p class="MsoNormal"> LYS 1099.B 0.0867</p>
<p class="MsoNormal"> LYS 1110.B 0.0733</p>
<p class="MsoNormal"> LYS 1115.B 0.0733</p>
<p class="MsoNormal"> LYS 1119.B 0.2148</p>
<p class="MsoNormal"> ASP 1124.B -0.2088</p>
<p class="MsoNormal"> PHE 1128.B 0.0352</p>
<p class="MsoNormal"> LYS 1131.B 0.0733</p>
<p class="MsoNormal"> ASP 1136.B -0.2088</p>
<p class="MsoNormal"> LYS 1138.B 0.0733</p>
<p class="MsoNormal"> GLU 1139.B -0.1137</p>
<p class="MsoNormal"> GLU 1144.B -0.1137</p>
<p class="MsoNormal"> LYS 1147.B 0.0733</p>
<p class="MsoNormal"> LYS 1148.B 0.0733</p>
<p class="MsoNormal"> LEU 1149.B -0.0471</p>
<p class="MsoNormal"> GLN 1154.B 0.0152</p>
<p class="MsoNormal">Correct charges are unknown for 9 non-standard atom names in otherwise standard residues</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Charges of 0.0 were assigned to the unknown atoms</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">1 model(s) had non-integral total charge</p>
<p class="MsoNormal">Details in reply log. </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">How do I work around this?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sid</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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