Fetal error in GROMACS

User discussions
1

GROMACS version:2023.4
GROMACS modification: Yes/No
Here post your question
I am trying run a simulation bit got this error.
Command line:
gmx pdb2gmx -f ddd.pdb -o leu.gro -water tip3p -ff charmm36-jul2021 -ter true

Using the Charmm36-jul2021 force field in directory ./charmm36-jul2021.ff

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 ddd.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 1862 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.

There are 3 chains and 0 blocks of water and 96 residues with 1862 atoms

chain #res #atoms

1 ‘A’ 1 1

2 ‘B’ 87 1853

3 ‘A’ 8 8

All occupancies are one

All occupancies are one
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

Back Off! I just backed up topol.top to ./#topol.top.1#

Processing chain 1 ‘A’ (1 atoms, 1 residues)

Residue MG590 has type ‘Ion’, assuming it is not linked into a chain.

Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
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 1 residues with 1 atoms
Chain time…

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

Making bonds…

No bonds

Generating angles, dihedrals and pairs…

Making cmap torsions…

There are 0 dihedrals, 0 impropers, 0 angles
0 pairs, 0 bonds and 0 virtual sites

Total mass 24.305 a.m.u.

Total charge 2.000 e

Writing topology

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

Processing chain 2 ‘B’ (1853 atoms, 87 residues)

Identified residue G1 as a starting terminus.

Identified residue A76 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for G-1
0: NH3+
1: NH2
2: 5MET
3: 5PHO
4: 5POM
5: 5TER
6: None
5
Start terminus G-1: 5TER
Select end terminus type for A-76
0: COO-
1: COOH
2: CT1
3: CT2
4: 3TER
5: None
4
End terminus A-76: 3TER
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn

Checking for duplicate atoms…

Now there are 1847 atoms. Deleted 3 duplicates.

Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2023.4
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)

Fatal error:
Residue 56 named C of a molecule in the input file was mapped
to an entry in the topology database, but the atom C4’ 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 when using GROMACS - GROMACS 2024.3 documentation

I checked the data base, there is nothing missing. Here is the na.rtp file.
na.txt (412.8 KB)

I would be grateful if you kindly give me some suggestions in this regards.

Sincerely,
Ahsan

2

Have you checked residue 56 in chain B in the PDB file? What residue is that? Is it a standard residue?

3

Yes, I checked. Here is the 56th residue from the pdb file:
ATOM 1415 P C B 56 4.002 -18.060 41.559 1.00 42.82 B P
ATOM 1416 O1P C B 56 3.092 -17.125 42.252 1.00 42.92 B O
ATOM 1417 O2P C B 56 4.366 -19.314 42.254 1.00 43.60 B O
ATOM 1418 C5’ C B 56 2.004 -18.579 39.936 1.00 42.58 B C
ATOM 1419 O5’ C B 56 3.415 -18.416 40.107 1.00 42.39 B O
ATOM 1420 C4’ C B 56 1.378 -17.373 39.252 1.00 41.97 B C
ATOM 1421 O4’ C B 56 1.367 -16.181 40.069 1.00 41.92 B O
ATOM 1422 C3’ C B 56 2.133 -16.889 38.046 1.00 41.21 B C
ATOM 1423 O3’ C B 56 1.946 -17.821 37.018 1.00 41.21 B O
ATOM 1424 C2’ C B 56 1.463 -15.550 37.798 1.00 40.81 B C
ATOM 1425 O2’ C B 56 0.261 -15.659 37.067 1.00 40.84 B O
ATOM 1426 C1’ C B 56 1.191 -15.062 39.220 1.00 41.28 B C
ATOM 1427 N1 C B 56 2.097 -13.955 39.639 1.00 40.99 B N
ATOM 1428 C2 C B 56 2.031 -12.731 38.958 1.00 40.45 B C
ATOM 1429 O2 C B 56 1.226 -12.577 38.033 1.00 40.22 B O
ATOM 1430 N3 C B 56 2.861 -11.730 39.338 1.00 40.28 B N
ATOM 1431 C4 C B 56 3.723 -11.910 40.344 1.00 40.61 B C
ATOM 1432 N4 C B 56 4.517 -10.885 40.667 1.00 40.49 B N
ATOM 1433 C5 C B 56 3.813 -13.141 41.050 1.00 41.16 B C
ATOM 1434 C6 C B 56 2.993 -14.122 40.663 1.00 41.33 B C
ATOM 1435 P A B 57 3.186 -18.201 36.103 1.00 40.86 B P

Thank you so much for your response,

4

What residue is this? I didn’t find any residue, in the na.rtp file you sent, that matched the atom names/order in your pdb file.

5

Cytosine. I took the na.rpt from this file: charmm36-jul2021.ff

6

And where did you get the pdb file?

7

I got the PDB file from the protein database. I can send you that. Its 3zjv

8

I’m trying to help you, but you’re not making it easy. How did you get from 3zjv.pdb to ddd.pdb? 3zjv.pdb looks like this:

ATOM   7845  P     C B  56       4.002 -18.060  41.559  1.00 42.82           P  
ANISOU 7845  P     C B  56     4768   6989   4512  -1912   -550    359       P  
ATOM   7846  OP1   C B  56       3.092 -17.125  42.252  1.00 42.92           O  
ANISOU 7846  OP1   C B  56     4738   7125   4443  -1957   -495    305       O  
ATOM   7847  OP2   C B  56       4.366 -19.314  42.254  1.00 43.60           O  
ANISOU 7847  OP2   C B  56     4901   7057   4606  -1969   -608    470       O  
ATOM   7848  O5'   C B  56       3.415 -18.416  40.107  1.00 42.39           O  
ANISOU 7848  O5'   C B  56     4727   6849   4529  -1866   -540    319       O  
ATOM   7849  C5'   C B  56       2.004 -18.579  39.936  1.00 42.58           C  
ANISOU 7849  C5'   C B  56     4733   6918   4529  -1919   -514    299       C  
ATOM   7850  C4'   C B  56       1.378 -17.373  39.252  1.00 41.97           C  
ANISOU 7850  C4'   C B  56     4611   6887   4451  -1866   -457    201       C  
ATOM   7851  O4'   C B  56       1.367 -16.181  40.069  1.00 41.92           O  
ANISOU 7851  O4'   C B  56     4566   6978   4384  -1864   -412    158       O  
ATOM   7852  C3'   C B  56       2.133 -16.889  38.046  1.00 41.21           C  
ANISOU 7852  C3'   C B  56     4527   6706   4424  -1762   -454    151       C  
ATOM   7853  O3'   C B  56       1.946 -17.821  37.018  1.00 41.21           O  
ANISOU 7853  O3'   C B  56     4562   6617   4479  -1752   -480    164       O  
ATOM   7854  C2'   C B  56       1.463 -15.550  37.798  1.00 40.81           C  
ANISOU 7854  C2'   C B  56     4427   6728   4351  -1725   -393     67       C  
ATOM   7855  O2'   C B  56       0.261 -15.659  37.067  1.00 40.84           O  
ANISOU 7855  O2'   C B  56     4407   6749   4362  -1733   -376     42       O  
ATOM   7856  C1'   C B  56       1.191 -15.062  39.220  1.00 41.28           C  
ANISOU 7856  C1'   C B  56     4459   6897   4328  -1785   -367     73       C  
ATOM   7857  N1    C B  56       2.097 -13.955  39.639  1.00 40.99           N  
ANISOU 7857  N1    C B  56     4421   6879   4276  -1744   -346     34       N  
ATOM   7858  C2    C B  56       2.031 -12.731  38.958  1.00 40.45           C  
ANISOU 7858  C2    C B  56     4334   6809   4228  -1669   -299    -47       C  
ATOM   7859  O2    C B  56       1.226 -12.577  38.033  1.00 40.22           O  
ANISOU 7859  O2    C B  56     4284   6770   4228  -1633   -277    -81       O  
ATOM   7860  N3    C B  56       2.861 -11.730  39.338  1.00 40.28           N  
ANISOU 7860  N3    C B  56     4316   6796   4191  -1641   -280    -84       N  
ATOM   7861  C4    C B  56       3.723 -11.910  40.344  1.00 40.61           C  
ANISOU 7861  C4    C B  56     4376   6859   4196  -1687   -310    -44       C  
ATOM   7862  N4    C B  56       4.517 -10.885  40.667  1.00 40.49           N  
ANISOU 7862  N4    C B  56     4366   6856   4164  -1667   -293    -84       N  
ATOM   7863  C5    C B  56       3.813 -13.141  41.050  1.00 41.16           C  
ANISOU 7863  C5    C B  56     4460   6937   4243  -1758   -361     44       C  
ATOM   7864  C6    C B  56       2.993 -14.122  40.663  1.00 41.33           C  
ANISOU 7864  C6    C B  56     4482   6938   4283  -1783   -375     79       C

When removing the ANISOU lines:

ATOM   7845  P     C B  56       4.002 -18.060  41.559  1.00 42.82           P  
ATOM   7846  OP1   C B  56       3.092 -17.125  42.252  1.00 42.92           O  
ATOM   7847  OP2   C B  56       4.366 -19.314  42.254  1.00 43.60           O  
ATOM   7848  O5'   C B  56       3.415 -18.416  40.107  1.00 42.39           O  
ATOM   7849  C5'   C B  56       2.004 -18.579  39.936  1.00 42.58           C  
ATOM   7850  C4'   C B  56       1.378 -17.373  39.252  1.00 41.97           C  
ATOM   7851  O4'   C B  56       1.367 -16.181  40.069  1.00 41.92           O  
ATOM   7852  C3'   C B  56       2.133 -16.889  38.046  1.00 41.21           C  
ATOM   7853  O3'   C B  56       1.946 -17.821  37.018  1.00 41.21           O  
ATOM   7854  C2'   C B  56       1.463 -15.550  37.798  1.00 40.81           C  
ATOM   7855  O2'   C B  56       0.261 -15.659  37.067  1.00 40.84           O  
ATOM   7856  C1'   C B  56       1.191 -15.062  39.220  1.00 41.28           C  
ATOM   7857  N1    C B  56       2.097 -13.955  39.639  1.00 40.99           N  
ATOM   7858  C2    C B  56       2.031 -12.731  38.958  1.00 40.45           C  
ATOM   7859  O2    C B  56       1.226 -12.577  38.033  1.00 40.22           O  
ATOM   7860  N3    C B  56       2.861 -11.730  39.338  1.00 40.28           N  
ATOM   7861  C4    C B  56       3.723 -11.910  40.344  1.00 40.61           C  
ATOM   7862  N4    C B  56       4.517 -10.885  40.667  1.00 40.49           N  
ATOM   7863  C5    C B  56       3.813 -13.141  41.050  1.00 41.16           C  
ATOM   7864  C6    C B  56       2.993 -14.122  40.663  1.00 41.33           C

I don’t say for sure that restoring the atom order (see C5’ and O5’ compared to your output) will necessarily fix everything. But it’d be a good start. I would also have a close look at the ' vs ’ characters. They seem different in the original pdb and the na.txt file compared to your file.

9

Sorry, my bad.
I removed all other elements except the tRNA. Then, I matched it with 1ehz, which contains Mg, using Chimera. I selected the positions of the Mg ions with respect to my tRNA (3zjv), combined them, and then saved the structure. I also deleted the ANISOU lines.

10

Does it help if you reorder C5’ and O5’ and change " ’" to “'”?

11

Terminal Saved Output.txt (45.3 KB)

ddd.txt (189.6 KB)
No, I just reordered: O5’ then C5’ for the 56th residue only and changed " ’ " to “'” for all. I just open my pdb file in text document and saved as txt file. I also send both file (code and txt) to avoid misunderstanding.
Thank you so much for you kind cooperation.

12

It’s a bit confusing with the residue numbering. This is residue 56:

ATOM   1179  P   C   B  47H     -8.465 -14.381  21.806  1.00 41.41      B    P\
ATOM   1180  O1P C   B  47H     -8.762 -14.850  23.178  1.00 41.67      B    O\
ATOM   1181  O2P C   B  47H     -7.840 -13.055  21.586  1.00 40.74      B    O\
ATOM   1182  C5' C   B  47H     -7.925 -16.817  20.841  1.00 41.98      B    C\
ATOM   1183  O5' C   B  47H     -7.526 -15.466  21.095  1.00 41.29      B    O\
ATOM   1184  O4' C   B  47H     -7.190 -16.666  18.530  1.00 41.79      B    O\
ATOM   1185  O3' C   B  47H     -4.981 -18.234  20.903  1.00 41.21      B    O\
ATOM   1186  C2' C   B  47H     -5.013 -17.540  18.573  1.00 41.16      B    C\
ATOM   1187  O2' C   B  47H     -5.146 -18.884  18.148  1.00 41.86      B    O\
ATOM   1188  C1' C   B  47H     -5.956 -16.618  17.813  1.00 41.30      B    C\
ATOM   1189  N1  C   B  47H     -5.382 -15.210  17.639  1.00 40.55      B    N\
ATOM   1190  C2  C   B  47H     -4.307 -15.017  16.741  1.00 40.17      B    C\
ATOM   1191  N4  C   B  47H     -3.710 -11.564  17.011  1.00 38.89      B    N\
ATOM   1192  N3  C   B  47H     -3.784 -13.784  16.560  1.00 39.59      B    N\
ATOM   1193  C4  C   B  47H     -4.278 -12.749  17.232  1.00 39.39      B    C\
ATOM   1194  C5  C   B  47H     -5.366 -12.899  18.150  1.00 39.78      B    C\
ATOM   1195  C6  C   B  47H     -5.881 -14.130  18.324  1.00 40.34      B    C\
ATOM   1196  C1' C   B  47H     -5.525 -17.272  19.998  1.00 41.11      B    C\
ATOM   1197  C2  C   B  47H     -7.061 -17.379  20.011  1.00 41.11      B    C\
ATOM   1198  O2  C   B  47H     -3.836 -15.964  16.113  1.00 40.43      B    O\

It is indeed missing the C4’ atom. So, I’m afraid there is an error in the input. It also has two C1’ and two C2 as far as I can see. So, it’s probably missing some other atom as well, since the number of atoms in the residue is correct.

You might be able to just rename them, if you are sure you are picking the right ones.

13

Thank you so much.
One C1 was CM1 and C2 was CM2. I checked in the na.rpt file but could not find any replacement. That is why I renamed as C1 and C2

14

Sounds good. I hope you can find the correct names for them and that everything works after that.

15

I started from scratch again. Like downloaded, removing other atoms except tRNA. This time it showed an error for the other command:
Command: gmx grompp -f emin-charmm.mdp -c mm_solv.gro -p topol.top -o em.tpr
The largest distance between excluded atoms is 1.201 nm between atom 1166
and 1168, which is larger than the cut-off distance. This will lead to
missing long-range corrections in the forces and energies. If you expect
that minimization will bring such distances within the cut-off, you can ignore this warning.
Then I ignored and applied the following command:
gmx mdrun -v -deffnm em :
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
I corrected my the cut-off distance in my emin-charmm.mdp file then it is okay now.
emin-charmm.txt (1.5 KB)

16

Dear Magnus,

I hope you are doing well.

I know you might be busy, but I encountered an issue while attempting to equilibrate a system and received the following error message:
Fatal error:
2 particles communicated to PME rank 0 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I generated the `npt.tpr` file using the following command:
gmx grompp -f npt-charmm.mdp -c em.gro -r em.gro -p topol.top -o npt.tpr
``
[equil.txt|attachment](upload://fifwmrDLzIFWRDRXLfMh73lfCR2.txt) (822 Bytes)
[npt-charmm.txt|attachment](upload://rQpYhjDz6yPFwxvVQ8DUCAvxc1V.txt) (2.3 KB)
[npt.txt|attachment](upload://14P7fiLjtaSQVDShXljc0YdJ2JA.txt) (2.8 MB)

I have attached the `npt.tpr` file and my `equil.sh` script for your reference. I would greatly appreciate any suggestions you may have to help resolve this issue.

Sincerely,
Ahsan
[npt-charmm.txt|attachment](upload://rQpYhjDz6yPFwxvVQ8DUCAvxc1V.txt) (2.3 KB)
17

Your uploads ended up inside a block of preformatted text, so I can’t access them.

In general, I would suggest running an NVT equilibration stage (with restraints and possibly a shorter time step) before NPT.

18

Thank you so much for the suggestion. I am going to try it.
I have attached the npt, npt-charmm and my equilibration script for your reference.
npt.txt (2.8 MB)
equil.txt (822 Bytes)
npt-charmm.txt (2.3 KB)

19

Here I have attached a nvt-charmm for your reference:
nvt-charmm.txt (1.9 KB)

Sincerely,
Ahsan