[Chimera-users] Non-standard atom names

Sid Majaha sidumomajaha at live.com
Mon Apr 15 01:18:58 PDT 2019

Hi Eric

Thank you so much for your help. I was able to see as well that my protein might have been too large for the calculations of the charges to take place efficiently because after following the procedure you gave me, it took a much longer time than using Gasteiger. Thank you so much for your help.


Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Saturday, April 13, 2019 2:18:39 AM
To: Sid Majaha
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Non-standard atom names

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 Pettersen
UCSF Computer Graphics Lab

On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha at live.com<mailto:sidumomajaha at live.com>> wrote:

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) Welcome to antechamber 17.3: molecular input file processor.


(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) 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) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out


(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) 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


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?


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