[Chimera-users] Non-standard atom names
Sid Majaha
sidumomajaha at live.com
Thu Apr 11 20:26:39 PDT 2019
Hi Eric
Problems with atom names in adding charge to a receptor using Chimera v1.13.1
(Tools-->Surface Binding/Analysis-->Add 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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