[Chimera-users] Non-standard atom names
Eric Pettersen
pett at cgl.ucsf.edu
Fri Apr 12 11:18:39 PDT 2019
Hi Sid,
The 2BXF structure has many, many missing heavy side-chain atoms. I recommend using the Dock Prep tool (Tools→Structure Editing→Dock Prep), which will use a rotamer library to fill out missing/incomplete side chains before adding hydrogens and assigning charges. Use the dialog check boxes to turn off any Dock Prep steps you don’t want (e.g. Write Mol2 file). Applying a lot of rotamers takes a few minutes, so you might want to bring up the Reply Log first (Favorites→Reply Log) so you can keep an eye on the Dock Prep progress while you possibly do something else.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
> On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha at live.com> wrote:
>
>
> Hi Eric
>
> Problems with atom names in adding charge to a receptor using Chimera v1.13.1
> (ToolsàSurface Binding/AnalysisàAdd charge)
> I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF.
> Net Charge is +0 for the residue HIS using charge method AM1_BCC
>
> Chimera warning received
> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues.
> Charges of 0.0 were assigned to the unknown atoms.
> 1 model(s) had non-intergral total charge.
>
> Reply log is as follows,
>
> Charge model: AMBER ff14SB
> Assigning partial charges to residue HIS (net charge +0) with am1-bcc method
> 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
> (HIS)
>
> (HIS) Welcome to antechamber 17.3: molecular input file processor.
>
> (HIS)
>
> (HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2).
>
> (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
>
> (HIS)
>
> (HIS)
>
> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> (HIS) Info: Total number of electrons: 78; net charge: 0
>
> (HIS)
>
> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out
>
> (HIS)
>
> (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
>
> (HIS)
>
> (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
>
> (HIS)
>
> Charges for residue HIS determined
> Non-standard atom names:
> VAL HB1 (VAL 551.A HB1)
> VAL HB2 (VAL 551.A HB2)
> ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3)
> VAL HB3 (VAL 551.A HB3)
> ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2)
> THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1)
> ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1)
> THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3)
> THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2)
> Total charge for #0: -66.402
> The following residues had non-integral charges:
> LYS 16.A 0.0867
> LEU 27.A -0.0471
> GLN 29.A 0.0392
> LYS 37.A 0.0867
> LYS 47.A 0.0733
> ASP 52.A -0.2088
> GLU 53.A -0.2103
> GLU 56.A -0.1137
> LYS 69.A 0.0867
> ARG 77.A 0.0612
> GLU 78.A -0.1137
> THR 79.A 0.3128
> TYR 80.A 0.0451
> GLU 82.A -0.1137
> GLN 90.A 0.0152
> GLU 91.A -0.1137
> GLU 93.A -0.1137
> ARG 94.A 0.0612
> PHE 98.A 0.0352
> GLN 100.A 0.0392
> ASN 107.A 0.0397
> ARG 110.A 0.0612
> LYS 132.A 0.0867
> LYS 133.A 0.2148
> LYS 155.A 0.0867
> LYS 158.A 0.0733
> GLN 166.A 0.0152
> LYS 170.A 0.0733
> LEU 174.A -0.0471
> LYS 186.A 0.0867
> GLN 200.A 0.0152
> LYS 201.A 0.0733
> ARG 205.A 0.153
> LYS 221.A 0.0867
> LYS 229.A 0.0733
> LYS 236.A 0.0733
> LEU 247.A -0.0471
> LYS 272.A 0.0733
> GLU 273.A -0.1137
> GLU 276.A -0.1137
> LYS 277.A 0.0733
> GLU 281.A -0.1137
> LYS 282.A 0.0733
> GLU 293.A -0.1137
> LEU 298.A -0.0471
> LYS 309.A 0.0733
> LYS 319.A 0.0867
> ASP 320.A -0.2088
> LYS 355.A 0.0867
> ASP 361.A -0.2088
> LYS 368.A 0.0867
> LYS 374.A 0.0733
> GLU 378.A -0.1137
> GLU 392.A -0.1137
> GLN 393.A 0.0152
> LYS 398.A 0.0733
> LEU 404.A -0.0471
> LYS 428.A 0.0867
> LYS 432.A 0.0867
> LYS 462.A 0.0733
> LYS 496.A 0.0867
> GLU 497.A -0.2103
> ASN 499.A 0.0397
> ILE 509.A 0.0431
> LYS 515.A 0.0733
> GLU 516.A -0.1137
> LYS 520.A 0.0733
> LEU 528.A -0.0471
> LYS 532.A 0.0733
> LYS 534.A 0.0733
> LYS 537.A 0.0733
> LYS 541.A 0.0733
> PHE 547.A 0.0352
> VAL 551.A 0.1935
> LYS 553.A 0.2148
> LYS 556.A 0.0733
> ASP 558.A -0.2088
> LYS 560.A 0.0733
> GLU 561.A -0.1137
> GLU 566.A -0.2103
> LYS 569.A 0.0733
> LYS 570.A 0.0733
> GLN 576.A 0.0152
> LYS 586.B 0.0733
> LEU 605.B -0.0471
> GLN 606.B 0.0152
> THR 621.B 0.3128
> LYS 625.B 0.0733
> ASP 630.B -0.2088
> GLU 634.B -0.1137
> ASN 635.B 0.0397
> LYS 638.B 0.0867
> GLU 656.B -0.1137
> THR 657.B 0.3128
> TYR 658.B 0.0451
> GLU 660.B -0.1137
> MET 661.B 0.0564
> LYS 667.B 0.0733
> GLN 668.B 0.0152
> GLU 671.B -0.1137
> ARG 672.B 0.0612
> PHE 676.B 0.0352
> GLN 678.B 0.0152
> ARG 688.B 0.0612
> LEU 689.B -0.0471
> LYS 733.B 0.0733
> GLN 744.B 0.0152
> LYS 748.B 0.0733
> LEU 752.B -0.0471
> LYS 755.B 0.0733
> ARG 760.B 0.0612
> GLU 762.B -0.1137
> LYS 764.B 0.2148
> GLN 778.B 0.0152
> LYS 779.B 0.0867
> ARG 783.B 0.3792
> LYS 799.B 0.0867
> LYS 807.B 0.0733
> LYS 814.B 0.0733
> LEU 849.B -0.0471
> LYS 850.B 0.0733
> GLU 851.B -0.1137
> GLU 854.B -0.1137
> LYS 855.B 0.0867
> LYS 860.B 0.0733
> GLU 871.B -0.1137
> ASP 875.B -0.2088
> LYS 887.B 0.0733
> LYS 891.B 0.0733
> GLU 895.B -0.1137
> LYS 897.B 0.0867
> LYS 933.B 0.2148
> GLU 942.B -0.1137
> LYS 952.B 0.0867
> GLU 956.B -0.1137
> LYS 963.B 0.2148
> LYS 976.B 0.0867
> ARG 984.B 0.3792
> LYS 1010.B 0.0867
> LYS 1018.B 0.2148
> LYS 1040.B 0.0733
> GLU 1075.B -0.1137
> ASP 1086.B -0.2088
> ILE 1087.B 0.0431
> LYS 1093.B 0.0733
> GLU 1094.B -0.1137
> GLN 1096.B 0.0152
> LYS 1098.B 0.0867
> LYS 1099.B 0.0867
> LYS 1110.B 0.0733
> LYS 1115.B 0.0733
> LYS 1119.B 0.2148
> ASP 1124.B -0.2088
> PHE 1128.B 0.0352
> LYS 1131.B 0.0733
> ASP 1136.B -0.2088
> LYS 1138.B 0.0733
> GLU 1139.B -0.1137
> GLU 1144.B -0.1137
> LYS 1147.B 0.0733
> LYS 1148.B 0.0733
> LEU 1149.B -0.0471
> GLN 1154.B 0.0152
> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues
>
> Charges of 0.0 were assigned to the unknown atoms
>
> 1 model(s) had non-integral total charge
> Details in reply log.
>
> How do I work around this?
>
> Sid
>
>
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