# Fetal error in GROMACS

**URL:** <https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077>\
**Category:** User discussions\
**Created:** [September 2, 2024, 2:36pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077 "2024-09-02T14:36:04Z")\
**Posts on this page:** 19\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 2, 2024, 2:36pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/1 "2024-09-02T14:36:04Z")

</div>

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 2025.4 documentation](https://manual.gromacs.org/current/user-guide/run-time-errors.html)

I checked the data base, there is nothing missing. Here is the na.rtp file.  
[na.txt](https://gromacs.bioexcel.eu/uploads/short-url/hB42w52M4CCBmEts9mM6zgCFKdw.txt) (412.8 KB)

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

Sincerely,  
Ahsan

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 3, 2024, 8:44am UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/2 "2024-09-03T08:44:19Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 3, 2024, 1:26pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/3 "2024-09-03T13:26:41Z")

</div>

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,

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 3, 2024, 2:34pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/4 "2024-09-03T14:34:34Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 3, 2024, 3:48pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/5 "2024-09-03T15:48:02Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 3, 2024, 3:49pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/6 "2024-09-03T15:49:24Z")

</div>

And where did you get the pdb file?

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 3, 2024, 4:10pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/7 "2024-09-03T16:10:23Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 3, 2024, 5:02pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/8 "2024-09-03T17:02:17Z")

</div>

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:

```auto
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:

```auto
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.

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 4, 2024, 12:31pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/9 "2024-09-04T12:31:28Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 4, 2024, 12:34pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/10 "2024-09-04T12:34:49Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 4, 2024, 1:14pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/11 "2024-09-04T13:14:05Z")

</div>

[Terminal Saved Output.txt](https://gromacs.bioexcel.eu/uploads/short-url/pEon8M5djNENv4UMf9R9oqj2wiW.txt) (45.3 KB)

[ddd.txt](https://gromacs.bioexcel.eu/uploads/short-url/v8tXj0P2zs3e6jfvKh0hsBWzDnO.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.

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 4, 2024, 2:13pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/12 "2024-09-04T14:13:49Z")

</div>

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

```auto
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.

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 4, 2024, 3:24pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/13 "2024-09-04T15:24:21Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 4, 2024, 3:32pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/14 "2024-09-04T15:32:09Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 4, 2024, 6:09pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/15 "2024-09-04T18:09:46Z")

</div>

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](https://gromacs.bioexcel.eu/uploads/short-url/wpbqQdunFoXHriH5HnDnNDivb3d.txt) (1.5 KB)

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 17, 2024, 6:06pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/16 "2024-09-17T18:06:37Z")

</div>

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.

```auto
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)
```

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 18, 2024, 6:33am UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/17 "2024-09-18T06:33:41Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 18, 2024, 12:48pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/18 "2024-09-18T12:48:24Z")

</div>

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](https://gromacs.bioexcel.eu/uploads/short-url/14P7fiLjtaSQVDShXljc0YdJ2JA.txt) (2.8 MB)  
[equil.txt](https://gromacs.bioexcel.eu/uploads/short-url/fifwmrDLzIFWRDRXLfMh73lfCR2.txt) (822 Bytes)  
[npt-charmm.txt](https://gromacs.bioexcel.eu/uploads/short-url/rQpYhjDz6yPFwxvVQ8DUCAvxc1V.txt) (2.3 KB)

---

<div class="post-metadata">

**Author:** ![Ahsan](https://avatars.discourse-cdn.com/v4/letter/a/958977/32.png) [@Ahsan](https://gromacs.bioexcel.eu/u/Ahsan)\
**Post date:** [September 18, 2024, 1:07pm UTC](https://gromacs.bioexcel.eu/t/fetal-error-in-gromacs/10077/19 "2024-09-18T13:07:23Z")

</div>

Here I have attached a nvt-charmm for your reference:  
[nvt-charmm.txt](https://gromacs.bioexcel.eu/uploads/short-url/nXVNN5A5HzKgD6AXmV3t7So2XNO.txt) (1.9 KB)

Sincerely,  
Ahsan