Residue mapped into topology database but atom name not found in file?

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Here post your question

Hello,

I am trying to create a topology file for GROMACS but I keep running into this error.

Fatal error:

Residue 36 named GLY of a molecule in the input file was mapped

to an entry in the topology database, but the atom CB used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

I have tried so much: using Swiss pdb for fixing the structure using Quick and Dirty fix, energy minimization, doing ignh, etc but I keep getting an error no matter what. I am not even sure how to fix the atom naming. Can someone please help me with how I can fix this? Or can I continue with the Protein-Ligand complex simulation?

Hi,
GLY - usually labeled a glycine residue - and glycine does not have CB. The error says that you have CB in the GLY entry in the topology database, but not in the structure file.
Did you check if this was the case?
It could be that you have a modified GLY residues, then it is good to use another name for residue both in the topology database and in the structure file
I hope it helps
\Alessandra

The entire screen output from pdb2gmx (copied and pasted in its entirety please, no screen shots) would be very useful here in troubleshooting.

Hello,

This is what the screen outputs were from a couple of my attempts:

**

iMacPro-75569:5-methyl_test syedarizvi$ grep -v HOH 5MTR.pdb > 5MTR_clean.pdb
iMacPro-75569:5-methyl_test syedarizvi$ grep 5LIG 5MTR_clean.pdb > 5LIG.pdb
iMacPro-75569:5-methyl_test syedarizvi$ gmx pdb2gmx -f 5MTR_clean.pdb -o 5MTR_processed.gro -ignh
:-) GROMACS - gmx pdb2gmx, 2021 (-:

                        GROMACS is written by:
 Andrey Alekseenko              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      
Gilles Gouaillardet             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              Artem Zhmurov       
                       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) 2001-2019, 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 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/syedarizvi/Desktop/gromax/5-methyl_test
Command line:
gmx pdb2gmx -f 5MTR_clean.pdb -o 5MTR_processed.gro -ignh

Select the Force Field:

From current directory:

1: CHARMM36 all-atom force field

From ‘/usr/local/gromacs/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-jul2021 force field in directory ./charmm36-jul2021.ff
Opening force field file ./charmm36-jul2021.ff/watermodels.dat

Select the Water Model:

1: TIP3P_CHARMM CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P 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-jul2021.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2021.ff/aminoacids.r2b

going to rename ./charmm36-jul2021.ff/carb.r2b
Opening force field file ./charmm36-jul2021.ff/carb.r2b

going to rename ./charmm36-jul2021.ff/cgenff.r2b
Opening force field file ./charmm36-jul2021.ff/cgenff.r2b

going to rename ./charmm36-jul2021.ff/ethers.r2b
Opening force field file ./charmm36-jul2021.ff/ethers.r2b

going to rename ./charmm36-jul2021.ff/lipid.r2b
Opening force field file ./charmm36-jul2021.ff/lipid.r2b

going to rename ./charmm36-jul2021.ff/metals.r2b
Opening force field file ./charmm36-jul2021.ff/metals.r2b

going to rename ./charmm36-jul2021.ff/na.r2b
Opening force field file ./charmm36-jul2021.ff/na.r2b

going to rename ./charmm36-jul2021.ff/silicates.r2b
Opening force field file ./charmm36-jul2021.ff/silicates.r2b

going to rename ./charmm36-jul2021.ff/solvent.r2b
Opening force field file ./charmm36-jul2021.ff/solvent.r2b
Reading 5MTR_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 5371 atoms

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

There are 4 chains and 0 blocks of water and 677 residues with 5371 atoms

chain #res #atoms

1 ‘A’ 80 628

2 ‘A’ 221 1765

3 ‘A’ 36 281

4 ‘A’ 340 2697

there were 0 atoms with zero occupancy and 16 atoms with occupancy unequal to one (out of 5371 atoms). Check your pdb file.

there were 0 atoms with zero occupancy and 16 atoms with occupancy unequal to one (out of 5371 atoms). Check your pdb file.
Opening force field file ./charmm36-jul2021.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2021)
Opening force field file ./charmm36-jul2021.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2021.ff/carb.rtp
Opening force field file ./charmm36-jul2021.ff/cgenff.rtp
Opening force field file ./charmm36-jul2021.ff/ethers.rtp
Opening force field file ./charmm36-jul2021.ff/lipid.rtp
Opening force field file ./charmm36-jul2021.ff/metals.rtp
Opening force field file ./charmm36-jul2021.ff/na.rtp
Opening force field file ./charmm36-jul2021.ff/silicates.rtp
Opening force field file ./charmm36-jul2021.ff/solvent.rtp
Opening force field file ./charmm36-jul2021.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2021.ff/carb.hdb
Opening force field file ./charmm36-jul2021.ff/cgenff.hdb
Opening force field file ./charmm36-jul2021.ff/ethers.hdb
Opening force field file ./charmm36-jul2021.ff/lipid.hdb
Opening force field file ./charmm36-jul2021.ff/metals.hdb
Opening force field file ./charmm36-jul2021.ff/na.hdb
Opening force field file ./charmm36-jul2021.ff/silicates.hdb
Opening force field file ./charmm36-jul2021.ff/solvent.hdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2021.ff/carb.n.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2021.ff/metals.n.tdb
Opening force field file ./charmm36-jul2021.ff/na.n.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2021.ff/carb.c.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2021.ff/metals.c.tdb
Opening force field file ./charmm36-jul2021.ff/na.c.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.c.tdb

Processing chain 1 ‘A’ (628 atoms, 80 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 128 donors and 117 acceptors were found.
There are 178 hydrogen bonds
Will use HISE for residue 13
Will use HISE for residue 37

Identified residue MET1 as a starting terminus.

Identified residue PRO80 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 CYS5 CYS9 HIS13 MET18 MET20 HIS37
SD7 SG37 SG64 NE293 SD129 SD145 NE2282
CYS5 SG37 1.673
CYS9 SG64 2.472 0.916
HIS13 NE293 3.568 2.316 1.470
MET18 SD129 2.422 1.014 0.324 1.328
MET20 SD145 2.569 1.682 1.225 1.162 1.033
HIS37 NE2282 3.628 1.961 1.333 1.953 1.547 2.374
CYS79 SG620 4.473 2.909 2.020 1.418 2.058 2.433 1.400

Start terminus MET-1: NH3+
End terminus PRO-80: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 80 residues with 1270 atoms
Chain time…

Making bonds…

Number of bonds was 1281, now 1281

Generating angles, dihedrals and pairs…
Before cleaning: 3360 pairs
Before cleaning: 3395 dihedrals
Keeping all generated dihedrals

Making cmap torsions…

There are 78 cmap torsion pairs

There are 3395 dihedrals, 221 impropers, 2322 angles
3345 pairs, 1281 bonds and 0 virtual sites

Total mass 9004.521 a.m.u.

Total charge 4.000 e

Writing topology

Processing chain 2 ‘A’ (1765 atoms, 221 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 314 donors and 329 acceptors were found.
There are 426 hydrogen bonds
Will use HISE for residue 125
Will use HISD for residue 127
Will use HISE for residue 212
Will use HISE for residue 262
Will use HISE for residue 269
Will use HISE for residue 278
Will use HISE for residue 282

Identified residue SER86 as a starting terminus.

Identified residue PRO306 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET100 HIS125 HIS127 MET164 MET167 MET172 MET178
SD111 NE2322 NE2340 SD630 SD652 SD688 SD731
HIS125 NE2322 1.979
HIS127 NE2340 3.139 1.281
MET164 SD630 2.710 1.796 1.880
MET167 SD652 2.546 2.469 2.984 1.207
MET172 SD688 4.179 3.793 3.866 2.089 1.641
MET178 SD731 3.522 3.552 3.650 2.026 1.800 1.871
HIS212 NE2995 3.084 3.282 3.730 1.875 0.852 1.348 1.436
MET238 SD1198 1.228 2.820 3.992 3.070 2.405 3.952 3.581
HIS262 NE21409 2.634 2.911 3.472 1.688 0.569 1.690 1.610
HIS269 NE21462 3.146 2.380 2.677 1.235 1.146 1.717 2.623
HIS278 NE21543 3.466 2.664 2.888 1.497 1.390 1.635 2.777
CYS281 SG1567 3.968 3.156 3.014 1.443 1.619 0.974 2.014
HIS282 NE21577 4.258 3.278 2.828 1.610 2.200 1.656 1.992
CYS295 SG1679 3.844 3.518 3.487 1.767 1.634 1.124 0.871
CYS296 SG1685 3.522 2.955 2.927 1.166 1.247 1.078 1.350
CYS297 SG1691 4.094 3.474 3.244 1.699 1.914 1.269 1.327
HIS212 MET238 HIS262 HIS269 HIS278 CYS281 HIS282
NE2995 SD1198 NE21409 NE21462 NE21543 SG1567 NE21577
MET238 SD1198 2.748
HIS262 NE21409 0.458 2.327
HIS269 NE21462 1.780 3.097 1.662
HIS278 NE21543 1.915 3.369 1.861 0.332
CYS281 SG1567 1.786 4.004 1.938 1.309 1.255
HIS282 NE21577 2.356 4.503 2.493 2.024 2.030 0.898
CYS295 SG1679 1.353 3.857 1.622 2.112 2.185 1.221 1.306
CYS296 SG1685 1.345 3.597 1.476 1.472 1.564 0.708 1.021
CYS297 SG1691 1.830 4.218 2.048 2.102 2.140 0.974 0.749
CYS295 CYS296
SG1679 SG1685
CYS296 SG1685 0.701
CYS297 SG1691 0.586 0.694
Start terminus SER-86: NH3+
End terminus PRO-306: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 221 residues with 3503 atoms
Chain time…

Making bonds…

Number of bonds was 3550, now 3550

Generating angles, dihedrals and pairs…
Before cleaning: 9356 pairs
Before cleaning: 9471 dihedrals
Keeping all generated dihedrals

Making cmap torsions…

There are 219 cmap torsion pairs

There are 9471 dihedrals, 577 impropers, 6439 angles
9281 pairs, 3550 bonds and 0 virtual sites

Total mass 25030.853 a.m.u.

Total charge -12.000 e

Writing topology

Processing chain 3 ‘A’ (281 atoms, 36 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 49 donors and 51 acceptors were found.
There are 72 hydrogen bonds
Will use HISE for residue 327

Identified residue VAL311 as a starting terminus.

Identified residue GLY346 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS319 HIS327
SG64 NE2125
HIS327 NE2125 1.000
MET334 SD187 1.532 1.296
Start terminus VAL-311: NH3+
End terminus GLY-346: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.


Program: gmx pdb2gmx, version 2021
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 36 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

iMacPro-75569:5-methyl_test syedarizvi$ grep -v HOH 5MTR.pdb > 5MTR_clean.pdb
iMacPro-75569:5-methyl_test syedarizvi$ grep 5LIG 5MTR_clean.pdb > 5LIG.pdb
iMacPro-75569:5-methyl_test syedarizvi$ gmx pdb2gmx -f 5MTR_clean.pdb -o 5MTR_processed.gro -ignh
:-) GROMACS - gmx pdb2gmx, 2021 (-:

                        GROMACS is written by:
 Andrey Alekseenko              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      
Gilles Gouaillardet             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              Artem Zhmurov       
                       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) 2001-2019, 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 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/syedarizvi/Desktop/gromax/5-methyl_test
Command line:
gmx pdb2gmx -f 5MTR_clean.pdb -o 5MTR_processed.gro -ignh

Select the Force Field:

From current directory:

1: CHARMM36 all-atom force field

From ‘/usr/local/gromacs/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-jul2021 force field in directory ./charmm36-jul2021.ff
Opening force field file ./charmm36-jul2021.ff/watermodels.dat

Select the Water Model:

1: TIP3P_CHARMM CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P 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-jul2021.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2021.ff/aminoacids.r2b

going to rename ./charmm36-jul2021.ff/carb.r2b
Opening force field file ./charmm36-jul2021.ff/carb.r2b

going to rename ./charmm36-jul2021.ff/cgenff.r2b
Opening force field file ./charmm36-jul2021.ff/cgenff.r2b

going to rename ./charmm36-jul2021.ff/ethers.r2b
Opening force field file ./charmm36-jul2021.ff/ethers.r2b

going to rename ./charmm36-jul2021.ff/lipid.r2b
Opening force field file ./charmm36-jul2021.ff/lipid.r2b

going to rename ./charmm36-jul2021.ff/metals.r2b
Opening force field file ./charmm36-jul2021.ff/metals.r2b

going to rename ./charmm36-jul2021.ff/na.r2b
Opening force field file ./charmm36-jul2021.ff/na.r2b

going to rename ./charmm36-jul2021.ff/silicates.r2b
Opening force field file ./charmm36-jul2021.ff/silicates.r2b

going to rename ./charmm36-jul2021.ff/solvent.r2b
Opening force field file ./charmm36-jul2021.ff/solvent.r2b
Reading 5MTR_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 5371 atoms

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.

There are 4 chains and 0 blocks of water and 677 residues with 5371 atoms

chain #res #atoms

1 ‘A’ 80 628

2 ‘A’ 221 1765

3 ‘A’ 36 281

4 ‘A’ 340 2697

there were 0 atoms with zero occupancy and 16 atoms with occupancy unequal to one (out of 5371 atoms). Check your pdb file.

there were 0 atoms with zero occupancy and 16 atoms with occupancy unequal to one (out of 5371 atoms). Check your pdb file.
Opening force field file ./charmm36-jul2021.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2021)
Opening force field file ./charmm36-jul2021.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2021.ff/carb.rtp
Opening force field file ./charmm36-jul2021.ff/cgenff.rtp
Opening force field file ./charmm36-jul2021.ff/ethers.rtp
Opening force field file ./charmm36-jul2021.ff/lipid.rtp
Opening force field file ./charmm36-jul2021.ff/metals.rtp
Opening force field file ./charmm36-jul2021.ff/na.rtp
Opening force field file ./charmm36-jul2021.ff/silicates.rtp
Opening force field file ./charmm36-jul2021.ff/solvent.rtp
Opening force field file ./charmm36-jul2021.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2021.ff/carb.hdb
Opening force field file ./charmm36-jul2021.ff/cgenff.hdb
Opening force field file ./charmm36-jul2021.ff/ethers.hdb
Opening force field file ./charmm36-jul2021.ff/lipid.hdb
Opening force field file ./charmm36-jul2021.ff/metals.hdb
Opening force field file ./charmm36-jul2021.ff/na.hdb
Opening force field file ./charmm36-jul2021.ff/silicates.hdb
Opening force field file ./charmm36-jul2021.ff/solvent.hdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2021.ff/carb.n.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2021.ff/metals.n.tdb
Opening force field file ./charmm36-jul2021.ff/na.n.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2021.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2021.ff/carb.c.tdb
Opening force field file ./charmm36-jul2021.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2021.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2021.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2021.ff/metals.c.tdb
Opening force field file ./charmm36-jul2021.ff/na.c.tdb
Opening force field file ./charmm36-jul2021.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2021.ff/solvent.c.tdb

Processing chain 1 ‘A’ (628 atoms, 80 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 128 donors and 117 acceptors were found.
There are 178 hydrogen bonds
Will use HISE for residue 13
Will use HISE for residue 37

Identified residue MET1 as a starting terminus.

Identified residue PRO80 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 CYS5 CYS9 HIS13 MET18 MET20 HIS37
SD7 SG37 SG64 NE293 SD129 SD145 NE2282
CYS5 SG37 1.673
CYS9 SG64 2.472 0.916
HIS13 NE293 3.568 2.316 1.470
MET18 SD129 2.422 1.014 0.324 1.328
MET20 SD145 2.569 1.682 1.225 1.162 1.033
HIS37 NE2282 3.628 1.961 1.333 1.953 1.547 2.374
CYS79 SG620 4.473 2.909 2.020 1.418 2.058 2.433 1.400

Start terminus MET-1: NH3+
End terminus PRO-80: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 80 residues with 1270 atoms
Chain time…

Making bonds…

Number of bonds was 1281, now 1281

Generating angles, dihedrals and pairs…
Before cleaning: 3360 pairs
Before cleaning: 3395 dihedrals
Keeping all generated dihedrals

Making cmap torsions…

There are 78 cmap torsion pairs

There are 3395 dihedrals, 221 impropers, 2322 angles
3345 pairs, 1281 bonds and 0 virtual sites

Total mass 9004.521 a.m.u.

Total charge 4.000 e

Writing topology

Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.1#

Processing chain 2 ‘A’ (1765 atoms, 221 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 314 donors and 329 acceptors were found.
There are 426 hydrogen bonds
Will use HISE for residue 125
Will use HISD for residue 127
Will use HISE for residue 212
Will use HISE for residue 262
Will use HISE for residue 269
Will use HISE for residue 278
Will use HISE for residue 282

Identified residue SER86 as a starting terminus.

Identified residue PRO306 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET100 HIS125 HIS127 MET164 MET167 MET172 MET178
SD111 NE2322 NE2340 SD630 SD652 SD688 SD731
HIS125 NE2322 1.979
HIS127 NE2340 3.139 1.281
MET164 SD630 2.710 1.796 1.880
MET167 SD652 2.546 2.469 2.984 1.207
MET172 SD688 4.179 3.793 3.866 2.089 1.641
MET178 SD731 3.522 3.552 3.650 2.026 1.800 1.871
HIS212 NE2995 3.084 3.282 3.730 1.875 0.852 1.348 1.436
MET238 SD1198 1.228 2.820 3.992 3.070 2.405 3.952 3.581
HIS262 NE21409 2.634 2.911 3.472 1.688 0.569 1.690 1.610
HIS269 NE21462 3.146 2.380 2.677 1.235 1.146 1.717 2.623
HIS278 NE21543 3.466 2.664 2.888 1.497 1.390 1.635 2.777
CYS281 SG1567 3.968 3.156 3.014 1.443 1.619 0.974 2.014
HIS282 NE21577 4.258 3.278 2.828 1.610 2.200 1.656 1.992
CYS295 SG1679 3.844 3.518 3.487 1.767 1.634 1.124 0.871
CYS296 SG1685 3.522 2.955 2.927 1.166 1.247 1.078 1.350
CYS297 SG1691 4.094 3.474 3.244 1.699 1.914 1.269 1.327
HIS212 MET238 HIS262 HIS269 HIS278 CYS281 HIS282
NE2995 SD1198 NE21409 NE21462 NE21543 SG1567 NE21577
MET238 SD1198 2.748
HIS262 NE21409 0.458 2.327
HIS269 NE21462 1.780 3.097 1.662
HIS278 NE21543 1.915 3.369 1.861 0.332
CYS281 SG1567 1.786 4.004 1.938 1.309 1.255
HIS282 NE21577 2.356 4.503 2.493 2.024 2.030 0.898
CYS295 SG1679 1.353 3.857 1.622 2.112 2.185 1.221 1.306
CYS296 SG1685 1.345 3.597 1.476 1.472 1.564 0.708 1.021
CYS297 SG1691 1.830 4.218 2.048 2.102 2.140 0.974 0.749
CYS295 CYS296
SG1679 SG1685
CYS296 SG1685 0.701
CYS297 SG1691 0.586 0.694
Start terminus SER-86: NH3+
End terminus PRO-306: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 221 residues with 3503 atoms
Chain time…

Making bonds…

Number of bonds was 3550, now 3550

Generating angles, dihedrals and pairs…
Before cleaning: 9356 pairs
Before cleaning: 9471 dihedrals
Keeping all generated dihedrals

Making cmap torsions…

There are 219 cmap torsion pairs

There are 9471 dihedrals, 577 impropers, 6439 angles
9281 pairs, 3550 bonds and 0 virtual sites

Total mass 25030.853 a.m.u.

Total charge -12.000 e

Writing topology

Back Off! I just backed up posre_Protein_chain_A2.itp to ./#posre_Protein_chain_A2.itp.1#

Processing chain 3 ‘A’ (281 atoms, 36 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 49 donors and 51 acceptors were found.
There are 72 hydrogen bonds
Will use HISE for residue 327

Identified residue VAL311 as a starting terminus.

Identified residue GLY346 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS319 HIS327
SG64 NE2125
HIS327 NE2125 1.000
MET334 SD187 1.532 1.296
Start terminus VAL-311: NH3+
End terminus GLY-346: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.


Program: gmx pdb2gmx, version 2021
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 36 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
-------------------------------------------------------**

This is a known issue in the latest CHARMM36 port. Change the [ COO- ] entry in aminoacids.c.tdb from

[ add ]
2   8   OT    C      CA     CB
  OC        15.999400  -0.6700  -1

to

[ add ]
2   8   OT    C      CA     N
  OC        15.999400  -0.6700  -1

and the problem will be fixed.

Hello,

I have tried following your suggestion and now I am getting the following output :

** Fatal error:

The residues in the chain D501–ALA346 do not have a consistent type. The

first residue has type ‘Other’, while residue MET1 is of type ‘Protein’.

Either there is a mistake in your chain, or it includes nonstandard residue

names that have not yet been added to the residuetypes.dat file in the GROMACS

library directory. If there are other molecules such as ligands, they should

not have the same chain ID as the adjacent protein chain since it’s a separate

molecule.**

I know I have to modify the residue types.dat folder, but I am not sure how because I wrote in D501 Protein, but that is giving me the same error

***Update: I have solved the above error. but I came back to my original error, which still occurs despite me changing the amino acid folder

This likely means you’re still calling the old force field. Again, when reporting pdb2gmx issues, please always include the entire screen output. There is a massive amount of diagnostic information provided.

Pardon my confusion. Should I not call the CHARMM36 forcefield (option 1)?

We don’t know anything about how your files are necessarily organized or where you’ve tried to make changes. “Option 1” corresponds to force fields found in the working directory, but changes to residuetypes.dat have nothing to do with the location of the force field. A modified copy of residuetypes.dat in the working directory (not within the force field subdirectory) will take precedence over one in $GMXLIB if you do not want to make system-wide modifications.