Interactive protonation assignment for IgG4 with the charmm36 force field

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:

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:

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.


$ 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

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check out http://www.gromacs.org for more information.

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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

Are you sure you want glutamine protonated? (gln, not glutamate glu)

That’s a very interesting suggestion I haven’t thought of before. Thanks. I will double check the pdb2pqr output and get back later.

I’ve never seen an instance in which Gln should be cationic. And in any case, CHARMM doesn’t support such a residue.