# Interactive protonation assignment for IgG4 with the charmm36 force field
**URL:** https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715
**Category:** User discussions
**Tags:** pdb2gmx, forcefield, mdrun
**Created:** [June 29, 2023, 3:48pm UTC](https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715 "2023-06-29T15:48:35Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@wintermute](https://gromacs.bioexcel.eu/u/wintermute)
#### Post date: [June 29, 2023, 3:48pm UTC](https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715/1 "2023-06-29T15:48:35Z")
GROMACS version: 2019.3
GROMACS modification: No
Here post your question
I have read posts regarding the protonation states with gromacs and the error pages about “residue xxx hasn’t been found” but didn’t find particular solutions to the problem I faced that was caused by the manual protonation so any ideas would be more than welcome.
I am testing the performance of an IgG4 antibody under different pHs and by achieving that I intend to change the protonation states of residues such as Arg, Glu, Asp etc. The force field I am using is the charmm36 July 2022 version.
Due to the need for simulations under different protonation states of the residues, I have to manually assign the protonation states to residues with `-inter`. I noticed it was the interactive protonation stage that gave me the error, since when I ran pdb2gmx without manual protonation it didn’t report errors. I found that it was caused by the stage when GROMACS asked if I want glutamine protonated:
```auto
Which GLUTAMINE type do you want for residue 3
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
```
And the error I got:
```auto
Program: gmx pdb2gmx, version 2019.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 618)
Fatal error:
Residue 'QLN' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
```
It seems to me that GROMACS built-in protonation does not fit with the charmm36, since obviously QLN is the naming rule for e.g. OPLS but not for charmm36 and thus in the topology files charmm36 offers it does not record such entries. I am pretty sure that my original pdb file does not have QLN inside and as I mentioned before, if I don’t use `-inter` to interactively assign protonation states I don’t have such error messages.
Therefore, I was wondering if the built-in user interactive protonation that GROMACS offered is somehow incompatible with the protonation of charmm force field, since from my understanding charmm force field uses patches to do protonation. If so, is there any solution to protonate the protein in gromacs with the charmm36 force field? Maybe it’s just my nativity but did not find too many posts around this question.
The full error page can be found below. I was told that perhaps the full page could provide more information for any troubleshooting.
```auto
$ gmx pdb2gmx -f mek5bmrb0c.pdb -o processed.gro -ignh -merge interactive -inter
:-) GROMACS - gmx pdb2gmx, 2019.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx pdb2gmx, version 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/IgG4A33/IgG4_230623_gromacs/TestCharmm36230623/TestWithManualProtonation270623
Command line:
gmx pdb2gmx -f mek5bmrb0c.pdb -o processed.gro -ignh -merge interactive -inter -noter
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From '/shared/ucl/apps/gromacs/2019.3/intel-2018/share/gromacs/top':
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff
Opening force field file ./charmm36-jul2022.ff/watermodels.dat
Select the Water Model:
1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)
2: TIP3P_ORIGINAL Original TIP3P water model
3: SPC SPC water model
4: SPCE SPC/E water model
5: TIP5P TIP5P water model
6: TIP4P TIP4P water model
7: TIP4PEW TIP4P/Ew water model
8: None
1
going to rename ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b
going to rename ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b
going to rename ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b
going to rename ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b
going to rename ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b
going to rename ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b
going to rename ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b
going to rename ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b
going to rename ./charmm36-jul2022.ff/solvent.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading mek5bmrb0c.pdb...
Read '', 10120 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue CYS213 (chain id 'A', atom 3248 OXT) and chain starting with
residue GLU1 (chain id 'B', atom 3254 N) into a single moleculetype (keeping termini)? [n/y]
y
Merge chain ending with residue LYS444 (chain id 'B', atom 9986 OXT) and chain starting with
residue ASP1 (chain id 'C', atom 10000 N) into a single moleculetype (keeping termini)? [n/y]
y
Merge chain ending with residue CYS213 (chain id 'C', atom 13246 OXT) and chain starting with
residue GLU1 (chain id 'D', atom 13252 N) into a single moleculetype (keeping termini)? [n/y]
y
Merged chains into joint molecule definitions at 3 places.
There are 1 chains and 0 blocks of water and 1314 residues with 10120 atoms
chain #res #atoms
1 'A' 1314 10120
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp
Atomtype 579
Reading residue database... (Charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Residue 540
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Residue 903
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Residue 1826
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Residue 1850
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Residue 2261
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Residue 2268
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/na.rtp
Residue 2346
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Residue 2351
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Residue 2427
Sorting it all out...
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb
Processing chain 1 'A' (10120 atoms, 1314 residues)
Which LYSINE type do you want for residue 24
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which LYSINE type do you want for residue 39
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which LYSINE type do you want for residue 42
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which LYSINE type do you want for residue 45
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which LYSINE type do you want for residue 103
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which LYSINE type do you want for residue 107
0. Not protonated (charge 0) (LSN)
1. Protonated (charge +1) (LYS)
Type a number:1
Which ARGININE type do you want for residue 1211
0. Not protonated (charge 0) (ARGN)
1. Protonated (charge +1) (ARG)
Type a number:1
Which ARGININE type do you want for residue 1276
0. Not protonated (charge 0) (ARGN)
1. Protonated (charge +1) (ARG)
Type a number:1
Which ARGININE type do you want for residue 1283
0. Not protonated (charge 0) (ARGN)
1. Protonated (charge +1) (ARG)
Type a number:1
Which GLUTAMINE type do you want for residue 3
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:1
Which GLUTAMINE type do you want for residue 6
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:0
Which GLUTAMINE type do you want for residue 27
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:0
Which GLUTAMINE type do you want for residue 37
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:0
Which GLUTAMINE type do you want for residue 38
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:1
Which GLUTAMINE type do you want for residue 79
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:1
Which GLUTAMINE type do you want for residue 90
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:1
Which GLUTAMINE type do you want for residue 100
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:1
Which GLUTAMINE type do you want for residue 124
0. Not protonated (charge 0) (GLN)
1. Protonated (charge +1) (QLN)
Type a number:0
Which ASPARTIC ACID type do you want for residue 739
0. Not protonated (charge -1) (ASP)
1. Protonated (charge 0) (ASPP)
Type a number:0
Which ASPARTIC ACID type do you want for residue 779
0. Not protonated (charge -1) (ASP)
1. Protonated (charge 0) (ASPP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 302
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 350
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 365
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 429
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 443
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 468
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 479
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 482
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 493
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 503
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 504
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 528
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 543
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 555
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 566
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 567
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 590
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 592
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 598
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 629
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 640
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 738
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 762
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 780
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 799
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 817
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 821
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 843
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Which GLUTAMIC ACID type do you want for residue 851
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:1
Which GLUTAMIC ACID type do you want for residue 869
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:1
Identified residue ASP1 as a starting terminus.
Identified residue CYS213 as a ending terminus.
Identified residue GLU1 as a starting terminus.
Identified residue LYS444 as a ending terminus.
Identified residue ASP1 as a starting terminus.
Identified residue CYS213 as a ending terminus.
Identified residue GLU1 as a starting terminus.
Identified residue LYS444 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
1Special Atom Distance matrix:
MET4 CYS23 CYS88 CYS133 CYS193 CYS213 CYS22
SD30 SG162 SG664 SG1012 SG1491 SG1642 SG1794
CYS23 SG162 0.586
CYS88 SG664 0.494 0.203
CYS133 SG1012 4.417 4.165 4.137
CYS193 SG1491 4.455 4.200 4.179 0.203
CYS213 SG1642 5.833 5.655 5.589 1.741 1.830
CYS22 SG1794 2.129 2.553 2.362 4.587 4.677 5.469
MET34 SD1881 1.981 2.437 2.247 4.982 5.072 5.931 0.571
MET83 SD2269 2.174 2.554 2.432 3.989 4.020 5.024 1.533
CYS96 SG2374 1.928 2.358 2.168 4.525 4.610 5.466 0.202
CYS131 SG2623 5.355 5.093 5.051 1.117 1.220 0.989 5.324
CYS144 SG2709 4.396 4.295 4.190 1.702 1.877 1.731 3.805
CYS200 SG3122 4.385 4.308 4.195 1.891 2.063 1.868 3.697
CYS223 SG3303 5.401 5.024 5.021 1.592 1.631 2.186 5.798
CYS226 SG3323 6.222 5.802 5.810 2.612 2.645 2.882 6.696
MET249 SD3497 10.901 10.574 10.524 7.086 7.171 5.914 10.655
CYS258 SG3566 8.681 8.308 8.286 4.744 4.798 3.959 8.767
CYS318 SG4064 8.777 8.396 8.379 4.832 4.880 4.085 8.901
MET355 SD4348 10.561 10.332 10.232 7.532 7.683 6.298 9.876
CYS364 SG4416 10.435 10.128 10.060 7.053 7.176 5.941 10.073
CYS422 SG4884 10.466 10.162 10.094 7.021 7.141 5.878 10.095
MET425 SD4904 10.701 10.380 10.325 6.977 7.072 5.806 10.419
MET4 SD5090 5.332 5.047 5.233 8.050 8.002 9.772 7.428
CYS23 SG5222 5.141 4.839 5.022 7.894 7.856 9.604 7.232
CYS88 SG5724 5.129 4.810 4.996 7.776 7.736 9.488 7.231
CYS133 SG6072 5.631 5.081 5.207 6.476 6.494 7.864 7.337
CYS193 SG6551 5.806 5.259 5.385 6.674 6.693 8.053 7.512
CYS213 SG6702 7.072 6.490 6.598 6.425 6.435 7.524 8.547
CYS22 SG6854 5.650 5.237 5.438 7.084 7.000 8.788 7.750
MET34 SD6941 5.820 5.432 5.635 7.330 7.241 9.041 7.923
MET83 SD7329 6.566 6.100 6.294 7.775 7.705 9.417 8.653
CYS96 SG7434 5.601 5.183 5.384 7.104 7.025 8.808 7.708
CYS131 SG7683 5.955 5.379 5.473 5.459 5.487 6.617 7.359
CYS144 SG7769 5.261 4.679 4.820 5.276 5.257 6.726 6.978
CYS200 SG8182 5.203 4.622 4.766 5.179 5.152 6.648 6.932
CYS223 SG8363 5.387 4.994 4.996 1.727 1.765 2.380 5.841
CYS226 SG8383 6.232 5.801 5.816 2.665 2.685 3.017 6.766
MET249 SD8557 7.634 7.313 7.240 5.330 5.496 4.877 7.431
CYS258 SG8626 6.486 6.083 6.058 3.432 3.546 3.378 6.731
CYS318 SG9124 6.285 5.883 5.857 3.266 3.383 3.273 6.535
MET355 SD9408 10.634 10.319 10.246 7.794 7.938 6.890 10.295
CYS364 SG9476 8.925 8.636 8.555 6.031 6.184 5.120 8.526
CYS422 SG9944 8.818 8.524 8.445 5.997 6.152 5.139 8.442
MET425 SD9964 7.847 7.539 7.462 5.352 5.516 4.761 7.574
MET34 MET83 CYS96 CYS131 CYS144 CYS200 CYS223
SD1881 SD2269 SG2374 SG2623 SG2709 SG3122 SG3303
MET83 SD2269 1.929
CYS96 SG2374 0.542 1.458
CYS131 SG2623 5.728 4.901 5.290
CYS144 SG2709 4.253 3.615 3.813 1.785
CYS200 SG3122 4.153 3.549 3.715 1.978 0.203
CYS223 SG3303 6.117 5.413 5.728 1.230 2.719 2.917
CYS226 SG3323 6.984 6.395 6.626 2.057 3.596 3.786 1.023
MET249 SD3497 10.997 10.659 10.666 5.991 7.070 7.167 5.953
CYS258 SG3566 9.102 8.578 8.740 3.740 5.184 5.332 3.432
CYS318 SG4064 9.234 8.693 8.871 3.847 5.327 5.478 3.497
MET355 SD4348 10.169 10.275 9.933 6.506 6.835 6.854 6.746
CYS364 SG4416 10.369 10.296 10.097 5.987 6.755 6.824 5.984
CYS422 SG4884 10.401 10.292 10.120 5.946 6.735 6.805 5.962
MET425 SD4904 10.752 10.474 10.434 5.882 6.885 6.975 5.863
MET4 SD5090 7.158 7.193 7.230 8.959 8.883 8.960 8.320
CYS23 SG5222 6.948 7.072 7.035 8.781 8.684 8.759 8.133
CYS88 SG5724 6.960 7.046 7.033 8.659 8.597 8.676 7.995
CYS133 SG6072 7.167 7.491 7.176 6.908 7.245 7.359 5.936
CYS193 SG6551 7.334 7.680 7.351 7.097 7.437 7.551 6.118
CYS213 SG6702 8.502 8.569 8.404 6.551 7.384 7.535 5.386
CYS22 SG6854 7.626 7.241 7.550 7.924 8.258 8.377 7.141
MET34 SD6941 7.796 7.376 7.721 8.192 8.510 8.627 7.434
MET83 SD7329 8.502 8.291 8.457 8.492 8.952 9.080 7.570
CYS96 SG7434 7.571 7.237 7.507 7.938 8.252 8.369 7.150
CYS131 SG7683 7.318 7.436 7.221 5.646 6.309 6.449 4.555
CYS144 SG7769 6.928 6.818 6.811 5.748 6.349 6.492 4.713
CYS200 SG8182 6.892 6.729 6.764 5.672 6.288 6.433 4.642
CYS223 SG8363 6.145 5.480 5.768 1.420 2.848 3.045 0.203
CYS226 SG8383 7.048 6.439 6.691 2.175 3.725 3.917 1.083
MET249 SD8557 7.610 7.924 7.437 4.573 4.871 4.926 4.392
CYS258 SG8626 6.970 6.780 6.686 2.726 3.741 3.886 2.105
CYS318 SG9124 6.774 6.582 6.489 2.595 3.576 3.722 1.971
MET355 SD9408 10.516 10.732 10.320 6.819 7.375 7.428 6.706
CYS364 SG9476 8.779 8.909 8.552 5.069 5.526 5.576 5.083
CYS422 SG9944 8.685 8.845 8.467 5.055 5.496 5.547 5.040
MET425 SD9964 7.779 8.031 7.586 4.531 4.861 4.914 4.424
CYS226 MET249 CYS258 CYS318 MET355 CYS364 CYS422
SG3323 SD3497 SG3566 SG4064 SD4348 SG4416 SG4884
MET249 SD3497 5.296
CYS258 SG3566 2.689 2.696
CYS318 SG4064 2.723 2.741 0.203
MET355 SD4348 6.370 3.081 4.608 4.760
CYS364 SG4416 5.398 1.573 3.247 3.358 1.750
CYS422 SG4884 5.382 1.410 3.175 3.285 1.804 0.203
MET425 SD4904 5.228 0.416 2.719 2.789 2.696 1.168 1.001
MET4 SD5090 8.719 13.857 11.345 11.357 14.203 13.589 13.640
CYS23 SG5222 8.519 13.614 11.132 11.147 13.903 13.309 13.364
CYS88 SG5724 8.372 13.474 10.983 10.996 13.800 13.186 13.241
CYS133 SG6072 5.887 10.309 8.088 8.092 10.667 9.911 9.996
CYS193 SG6551 6.051 10.424 8.222 8.225 10.780 10.019 10.107
CYS213 SG6702 4.959 8.827 6.697 6.659 9.663 8.617 8.695
CYS22 SG6854 7.428 12.598 9.993 9.974 13.374 12.544 12.576
MET34 SD6941 7.740 12.926 10.309 10.289 13.716 12.887 12.917
MET83 SD7329 7.686 12.643 10.113 10.080 13.478 12.567 12.613
CYS96 SG7434 7.431 12.589 9.996 9.979 13.330 12.511 12.546
CYS131 SG7683 4.283 8.493 6.286 6.281 9.080 8.182 8.260
CYS144 SG7769 4.695 9.506 7.065 7.054 10.213 9.327 9.381
CYS200 SG8182 4.646 9.515 7.047 7.034 10.252 9.361 9.410
CYS223 SG8363 0.925 5.980 3.444 3.503 6.781 5.996 5.980
CYS226 SG8383 0.204 5.418 2.786 2.808 6.548 5.548 5.532
MET249 SD8557 4.030 4.461 3.793 3.944 3.580 3.355 3.479
CYS258 SG8626 1.570 4.688 2.576 2.679 5.202 4.374 4.406
CYS318 SG9124 1.516 4.861 2.729 2.832 5.324 4.539 4.570
MET355 SD9408 6.110 3.085 4.398 4.505 1.951 1.633 1.832
CYS364 SG9476 4.649 3.106 3.389 3.552 2.009 1.806 1.925
CYS422 SG9944 4.604 3.259 3.441 3.602 2.170 1.965 2.092
MET425 SD9964 4.059 4.115 3.591 3.751 3.194 2.991 3.108
MET425 MET4 CYS23 CYS88 CYS133 CYS193 CYS213
SD4904 SD5090 SG5222 SG5724 SG6072 SG6551 SG6702
MET4 SD5090 13.730
CYS23 SG5222 13.478 0.435
CYS88 SG5724 13.343 0.464 0.203
CYS133 SG6072 10.160 4.515 4.177 4.063
CYS193 SG6551 10.274 4.558 4.218 4.108 0.204
CYS213 SG6702 8.733 6.420 6.153 6.003 2.283 2.292
CYS22 SG6854 12.526 2.187 2.300 2.105 4.037 4.111 5.289
MET34 SD6941 12.858 2.143 2.326 2.143 4.401 4.471 5.654
MET83 SD7329 12.573 2.741 2.748 2.566 3.514 3.526 4.630
CYS96 SG7434 12.511 2.062 2.150 1.952 3.888 3.958 5.201
CYS131 SG7683 8.363 6.017 5.722 5.583 1.878 1.979 1.207
CYS144 SG7769 9.404 4.654 4.418 4.256 1.704 1.863 2.163
CYS200 SG8182 9.418 4.611 4.390 4.223 1.884 2.044 2.310
CYS223 SG8363 5.888 8.207 8.016 7.877 5.754 5.935 5.184
CYS226 SG8383 5.359 8.611 8.416 8.266 5.792 5.956 4.840
MET249 SD8557 4.118 10.788 10.465 10.368 7.150 7.260 6.398
CYS258 SG8626 4.512 9.255 8.994 8.866 5.932 6.077 5.023
CYS318 SG9124 4.684 9.099 8.838 8.711 5.832 5.981 4.992
MET355 SD9408 2.720 13.645 13.327 13.218 9.727 9.812 8.511
CYS364 SG9476 2.713 12.264 11.961 11.854 8.663 8.776 7.686
CYS422 SG9944 2.871 12.123 11.816 11.711 8.499 8.611 7.537
MET425 SD9964 3.762 11.100 10.784 10.685 7.509 7.623 6.714
CYS22 MET34 MET83 CYS96 CYS131 CYS144 CYS200
SG6854 SD6941 SD7329 SG7434 SG7683 SG7769 SG8182
MET34 SD6941 0.379
MET83 SD7329 1.386 1.573
CYS96 SG7434 0.202 0.515 1.296
CYS131 SG7683 5.054 5.432 4.671 4.960
CYS144 SG7769 3.476 3.852 3.276 3.398 1.620
CYS200 SG8182 3.369 3.742 3.226 3.300 1.778 0.203
CYS223 SG8363 7.022 7.319 7.423 7.027 4.356 4.537 4.469
CYS226 SG8383 7.286 7.597 7.535 7.292 4.187 4.567 4.515
MET249 SD8557 10.094 10.449 10.127 10.027 5.685 6.868 6.932
CYS258 SG8626 8.218 8.557 8.352 8.185 4.286 5.136 5.146
CYS318 SG9124 8.081 8.419 8.238 8.048 4.218 5.029 5.037
MET355 SD9408 12.773 13.132 12.684 12.715 8.101 9.421 9.488
CYS364 SG9476 11.429 11.777 11.493 11.379 7.075 8.222 8.268
CYS422 SG9944 11.305 11.655 11.358 11.253 6.923 8.086 8.135
MET425 SD9964 10.369 10.721 10.427 10.307 6.012 7.163 7.220
CYS223 CYS226 MET249 CYS258 CYS318 MET355 CYS364
SG8363 SG8383 SD8557 SG8626 SG9124 SD9408 SG9476
CYS226 SG8383 0.970
MET249 SD8557 4.344 4.189
CYS258 SG8626 2.020 1.717 2.479
CYS318 SG9124 1.884 1.666 2.553 0.203
MET355 SD9408 6.683 6.257 3.042 4.797 4.954
CYS364 SG9476 5.081 4.822 1.669 3.314 3.438 1.853
CYS422 SG9944 5.031 4.775 1.482 3.229 3.352 1.891 0.204
MET425 SD9964 4.392 4.227 0.427 2.551 2.637 2.790 1.271
CYS422
SG9944
MET425 SD9964 1.095
Link CYS-23 SG-162 and CYS-88 SG-664 (y/n) ?y
Link CYS-133 SG-1012 and CYS-193 SG-1491 (y/n) ?y
Link CYS-22 SG-1794 and CYS-96 SG-2374 (y/n) ?y
Link CYS-144 SG-2709 and CYS-200 SG-3122 (y/n) ?y
Link CYS-223 SG-3303 and CYS-223 SG-8363 (y/n) ?y
Link CYS-226 SG-3323 and CYS-226 SG-8383 (y/n) ?y
Link CYS-258 SG-3566 and CYS-318 SG-4064 (y/n) ?y
Link CYS-364 SG-4416 and CYS-422 SG-4884 (y/n) ?y
Link CYS-23 SG-5222 and CYS-88 SG-5724 (y/n) ?y
Link CYS-133 SG-6072 and CYS-193 SG-6551 (y/n) ?y
Link CYS-22 SG-6854 and CYS-96 SG-7434 (y/n) ?y
Link CYS-144 SG-7769 and CYS-200 SG-8182 (y/n) ?y
Link CYS-258 SG-8626 and CYS-318 SG-9124 (y/n) ?y
Link CYS-364 SG-9476 and CYS-422 SG-9944 (y/n) ?y
Select start terminus type for ASP-1
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
0
Start terminus ASP-1: NH3+
Select end terminus type for CYS-213
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus CYS-213: COO-
Select start terminus type for GLU-1
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
0
Start terminus GLU-1: NH3+
Select end terminus type for LYS-444
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus LYS-444: COO-
Select start terminus type for ASP-1
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
0
Start terminus ASP-1: NH3+
Select end terminus type for CYS-213
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus CYS-213: COO-
Select start terminus type for GLU-1
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
0
Start terminus GLU-1: NH3+
Select end terminus type for LYS-444
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus LYS-444: COO-
-------------------------------------------------------
Program: gmx pdb2gmx, version 2019.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 618)
Fatal error:
Residue 'QLN' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
```
---
### Author:  [@ebriand](https://gromacs.bioexcel.eu/u/ebriand)
#### Post date: [June 30, 2023, 9:38am UTC](https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715/2 "2023-06-30T09:38:53Z")
Are you sure you want glut **amine** protonated? (`gln`, not glutamate `glu`)
---
### Author:  [@wintermute](https://gromacs.bioexcel.eu/u/wintermute)
#### Post date: [July 3, 2023, 9:17pm UTC](https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715/3 "2023-07-03T21:17:43Z")
That’s a very interesting suggestion I haven’t thought of before. Thanks. I will double check the pdb2pqr output and get back later.
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [July 3, 2023, 9:32pm UTC](https://gromacs.bioexcel.eu/t/interactive-protonation-assignment-for-igg4-with-the-charmm36-force-field/6715/4 "2023-07-03T21:32:02Z")
I’ve never seen an instance in which Gln should be cationic. And in any case, CHARMM doesn’t support such a residue.