# Residue mapped into topology database but atom name not found in file?
**URL:** https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675
**Category:** User discussions
**Created:** [February 15, 2022, 6:28pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675 "2022-02-15T18:28:25Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@Syeda](https://gromacs.bioexcel.eu/u/Syeda)
#### Post date: [February 15, 2022, 6:28pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/1 "2022-02-15T18:28:25Z")
GROMACS version:
GROMACS modification: Yes/No
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?
---
### Author:  [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)
#### Post date: [February 16, 2022, 1:27pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/2 "2022-02-16T13:27:17Z")
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
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [February 17, 2022, 4:24am UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/3 "2022-02-17T04:24:23Z")
The entire screen output from `pdb2gmx` (copied and pasted in its entirety please, no screen shots) would be very useful here in troubleshooting.
---
### Author:  [@Syeda](https://gromacs.bioexcel.eu/u/Syeda)
#### Post date: [February 17, 2022, 3:34pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/4 "2022-02-17T15:34:15Z")
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](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 [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)
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](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 [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)
-------------------------------------------------------\*\*
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [February 18, 2022, 4:38am UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/5 "2022-02-18T04:38:57Z")
This is a known issue in the latest CHARMM36 port. Change the `[COO-]` entry in `aminoacids.c.tdb` from
```auto
[add]
2 8 OT C CA CB
OC 15.999400 -0.6700 -1
```
to
```auto
[add]
2 8 OT C CA N
OC 15.999400 -0.6700 -1
```
and the problem will be fixed.
---
### Author:  [@Syeda](https://gromacs.bioexcel.eu/u/Syeda)
#### Post date: [February 18, 2022, 6:50pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/6 "2022-02-18T18:50:42Z")
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
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [February 19, 2022, 4:00pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/7 "2022-02-19T16:00:52Z")
> [@Syeda](#):
>
> \*\*\*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.
---
### Author:  [@Syeda](https://gromacs.bioexcel.eu/u/Syeda)
#### Post date: [February 28, 2022, 9:47pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/8 "2022-02-28T21:47:02Z")
Pardon my confusion. Should I not call the CHARMM36 forcefield (option 1)?
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [March 3, 2022, 1:31pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/9 "2022-03-03T13:31:34Z")
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.
---
### Author:  [@amei](https://gromacs.bioexcel.eu/u/amei)
#### Post date: [March 24, 2023, 9:45am UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/10 "2023-03-24T09:45:20Z")
hello：
This is my screen outputs. I have tried many times but it seems that the reason is TRP CH2 cannot be read? how can i change the name of TRP? just change the"TRP" to another amino acid name? how can i fix this bug? thank you!
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/home/z/Downloads/GMX/2023-CPU2/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\_ljpme-jul2022 force field in directory ./charmm36\_ljpme-jul2022.ff
Opening force field file ./charmm36\_ljpme-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\_ljpme-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/carb.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/carb.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/cgenff.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/ethers.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/ethers.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/lipid.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/lipid.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/metals.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/metals.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/na.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/na.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/silicates.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/silicates.r2b
going to rename ./charmm36\_ljpme-jul2022.ff/solvent.r2b
Opening force field file ./charmm36\_ljpme-jul2022.ff/solvent.r2b
Reading bestP34.pdb…
Read ‘’, 2884 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 370 residues with 2884 atoms
chain #res #atoms
1 ‘A’ 370 2884
All occupancies are one
All occupancies are one
Opening force field file ./charmm36\_ljpme-jul2022.ff/atomtypes.atp
Reading residue database… (Charmm36\_ljpme-jul2022)
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/carb.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/ethers.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/lipid.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/metals.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/na.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/silicates.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/solvent.rtp
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/carb.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/ethers.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/lipid.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/metals.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/na.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/silicates.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/solvent.hdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/na.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/na.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36\_ljpme-jul2022.ff/solvent.c.tdb
Processing chain 1 ‘A’ (2884 atoms, 370 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 528 donors and 554 acceptors were found.
There are 823 hydrogen bonds
Will use HISE for residue 23
Will use HISE for residue 51
Will use HISD for residue 56
Will use HISE for residue 58
Will use HISD for residue 86
Will use HISE for residue 88
Will use HISE for residue 125
Will use HISE for residue 163
Will use HISE for residue 203
Will use HISE for residue 272
Will use HISE for residue 292
Will use HISE for residue 362
Will use HISE for residue 367
Identified residue MET1 as a starting terminus.
Identified residue LEU370 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 HIS23 HIS51 HIS56 HIS58 MET78 HIS86
SD7 NE2168 NE2401 NE2442 NE2460 SD628 NE2691
HIS23 NE2168 4.310
HIS51 NE2401 4.908 0.919
HIS56 NE2442 6.019 2.742 1.929
HIS58 NE2460 6.724 3.389 2.475 1.410
MET78 SD628 6.462 2.215 1.992 3.173 3.286
HIS86 NE2691 6.517 2.336 2.285 3.546 3.759 0.499
HIS88 NE2707 6.039 1.832 1.847 3.220 3.594 0.679 0.549
MET120 SD964 6.917 3.813 4.186 5.105 6.009 3.547 3.163
CYS123 SG984 6.043 3.462 4.047 5.240 6.183 3.722 3.345
HIS125 NE21002 6.468 3.983 4.597 5.900 6.751 4.025 3.591
CYS147 SG1173 5.858 2.426 2.038 1.662 2.936 2.940 3.101
HIS163 NE21283 4.894 3.045 3.477 4.091 5.372 4.295 4.176
CYS181 SG1411 6.159 3.499 3.411 3.063 4.416 4.188 4.208
HIS203 NE21599 6.636 3.966 3.949 3.711 5.015 4.451 4.399
CYS221 SG1731 6.304 3.691 3.578 3.133 4.487 4.354 4.381
MET240 SD1880 6.923 3.296 3.481 4.277 5.087 2.688 2.355
HIS272 NE22128 6.256 2.028 1.658 2.316 2.918 1.308 1.462
CYS284 SG2216 6.587 2.418 2.351 3.282 3.807 1.209 1.005
HIS292 NE22277 5.800 1.862 1.775 2.488 3.420 1.973 1.982
CYS337 SG2627 6.483 2.369 2.381 3.390 3.955 1.308 1.050
MET339 SD2638 6.085 2.328 2.545 3.540 4.373 2.096 1.846
HIS362 NE22819 6.445 5.471 6.039 6.740 8.008 6.378 6.098
HIS367 NE22862 6.637 5.923 6.624 7.649 8.811 6.746 6.396
HIS88 MET120 CYS123 HIS125 CYS147 HIS163 CYS181
NE2707 SD964 SG984 NE21002 SG1173 NE21283 SG1411
MET120 SD964 3.001
CYS123 SG984 3.082 1.086
HIS125 NE21002 3.425 1.403 0.797
CYS147 SG1173 2.688 3.637 3.824 4.541
HIS163 NE21283 3.690 2.842 2.455 3.226 2.641
CYS181 SG1411 3.791 3.440 3.646 4.422 1.565 1.955
HIS203 NE21599 4.025 3.101 3.427 4.170 2.142 2.029 0.748
CYS221 SG1731 3.972 3.589 3.820 4.593 1.688 2.114 0.209
MET240 SD1880 2.221 1.035 1.796 2.199 2.926 2.958 3.078
HIS272 NE22128 1.167 3.129 3.404 3.923 1.683 3.383 2.926
CYS284 SG2216 0.896 2.459 2.829 3.215 2.441 3.495 3.349
HIS292 NE22277 1.546 2.647 2.816 3.446 1.303 2.517 2.247
CYS337 SG2627 0.895 2.295 2.630 3.015 2.484 3.369 3.329
MET339 SD2638 1.521 1.680 1.910 2.456 2.284 2.535 2.760
HIS362 NE22819 5.728 3.414 2.989 3.343 5.167 2.716 4.083
HIS367 NE22862 6.081 3.713 3.078 3.090 6.126 3.682 5.284
HIS203 CYS221 MET240 HIS272 CYS284 HIS292 CYS337
NE21599 SG1731 SD1880 NE22128 SG2216 NE22277 SG2627
CYS221 SG1731 0.736
MET240 SD1880 2.871 3.230
HIS272 NE22128 3.228 3.081 2.198
CYS284 SG2216 3.463 3.513 1.519 0.966
HIS292 NE22277 2.536 2.427 1.873 0.870 1.268
CYS337 SG2627 3.426 3.499 1.392 1.087 0.208 1.255
MET339 SD2638 2.790 2.944 0.973 1.512 1.060 1.060 0.897
HIS362 NE22819 3.676 4.161 4.199 5.645 5.391 4.824 5.224
HIS367 NE22862 4.911 5.394 4.656 6.273 5.850 5.520 5.658
MET339 HIS362
SD2638 NE22819
HIS362 NE22819 4.340
HIS367 NE22862 4.839 1.491
Linking CYS-181 SG-1411 and CYS-221 SG-1731…
Linking CYS-284 SG-2216 and CYS-337 SG-2627…
Select start terminus type for MET-1
0: MET1
1: NH3+
2: NH2
3: HYD1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
2
Start terminus MET-1: NH2
Select end terminus type for LEU-370
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
1
End terminus LEU-370: COOH
Opening force field file ./charmm36\_ljpme-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
* * *
Program: gmx pdb2gmx, version 2023
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)
Fatal error:
Residue 47 named TRP of a molecule in the input file was mapped
to an entry in the topology database, but the atom CH2 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 [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [March 26, 2023, 5:11pm UTC](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/11 "2023-03-26T17:11:25Z")
> [@amei](#):
>
> Residue 47 named TRP of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CH2 used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
Either your atom is named incorrectly in the input coordinate file or it’s missing. In the event of the former, rename it to CH2. If the latter, you need to model in any missing atoms using software outside of GROMACS before trying to run `pdb2gmx`. This is an extremely common error.