# Fatal error: -ter not working, atom C1 not found

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-ter-not-working-atom-c1-not-found/11501>\
**Category:** User discussions\
**Tags:** forcefield, mdrun\
**Created:** [February 10, 2025, 7:30am UTC](https://gromacs.bioexcel.eu/t/fatal-error-ter-not-working-atom-c1-not-found/11501 "2025-02-10T07:30:12Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![pia](https://avatars.discourse-cdn.com/v4/letter/p/6a8cbe/32.png) [@pia](https://gromacs.bioexcel.eu/u/pia)\
**Post date:** [February 10, 2025, 7:30am UTC](https://gromacs.bioexcel.eu/t/fatal-error-ter-not-working-atom-c1-not-found/11501/1 "2025-02-10T07:30:12Z")

</div>

GROMACS version:2023.3  
GROMACS modification: Yes/No

## I’m trying to perform MD simulation for viral protein-ligand complex. I used gmx pdb2gmx -ter for the protein after fatal error prompt (atom C1 not found in buiding block 1MET while combining tdb and rtp). I still get a fatal error prompt (Fatal error: atom O5’ not found in buiding block 1MET while combining tdb and rtp). What do I do?

Command line:  
gmx pdb2gmx -f protein\_clean.pdb -o protein\_processed.gro -ter

Force Field:

1: CHARMM all-atom force field

Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff  
Opening force field file ./charmm36-jul2022.ff/watermodels.dat

Select the Water Model:

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

There are 1 chains and 0 blocks of water and 345 residues with 3380 atoms

chain #res #atoms

1 ’ ’ 345 3380

All occupancies are one  
All occupancies are one  
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2022)

Back Off! I just backed up topol.top to ./#topol.top.6#

Processing chain 1 (3380 atoms, 345 residues)  
Analysing hydrogen-bonding network for automated assignment of histidine  
protonation. 524 donors and 519 acceptors were found.  
There are 710 hydrogen bonds  
Will use HISE for residue 20  
Will use HISE for residue 92  
Will use HISE for residue 103  
Will use HISE for residue 112  
Will use HISE for residue 191  
Will use HISE for residue 204  
Will use HISE for residue 225  
Will use HISE for residue 256  
Will use HISE for residue 290  
Will use HISE for residue 309

Identified residue MET1 as a starting terminus.

Identified residue THR345 as a ending terminus.  
8 out of 8 lines of specbond.dat converted successfully  
Special Atom Distance matrix:  
MET1 HIS20 CYS64 CYS82 HIS92 HIS103 CYS111  
SD8 NE2214 SG643 SG824 NE2917 NE21016 SG1085  
HIS20 NE2214 3.148  
CYS64 SG643 2.750 1.552  
CYS82 SG824 1.575 3.496 2.506  
HIS92 NE2917 1.849 1.753 2.049 2.849  
HIS103 NE21016 2.016 2.242 1.941 2.773 0.982  
CYS111 SG1085 0.811 3.154 2.477 0.801 2.249 2.337  
HIS112 NE21097 0.526 3.474 3.059 1.465 2.309 2.530 0.750  
MET162 SD1621 2.007 2.982 1.891 1.995 2.096 1.360 1.942  
MET177 SD1746 1.182 3.580 2.661 1.180 2.439 2.106 1.048  
MET184 SD1807 3.052 3.209 1.809 1.828 3.399 3.178 2.372  
CYS188 SG1852 3.394 3.215 2.284 2.251 3.743 3.844 2.678  
HIS191 NE21878 4.200 3.669 2.861 3.055 4.445 4.574 3.490  
HIS204 NE22004 3.352 2.760 1.409 2.377 3.299 3.131 2.761  
MET209 SD2046 3.374 3.924 2.538 1.922 4.006 3.755 2.627  
CYS220 SG2142 3.301 2.198 2.468 3.089 3.075 3.673 2.946  
HIS225 NE22193 4.065 2.308 2.561 3.698 3.601 4.096 3.668  
HIS256 NE22507 2.855 2.632 2.515 2.443 3.094 3.608 2.379  
MET259 SD2539 2.290 3.102 2.654 1.667 3.075 3.459 1.686  
CYS265 SG2593 3.589 3.152 2.761 2.781 3.848 4.216 2.974  
MET268 SD2619 3.083 2.571 2.667 2.801 3.167 3.755 2.677  
MET288 SD2813 1.460 3.648 2.690 1.549 2.455 1.959 1.445  
HIS290 NE22838 2.287 3.650 2.816 2.708 2.388 1.525 2.515  
HIS309 NE23045 3.265 1.990 2.501 4.099 1.510 1.472 3.627  
MET318 SD3122 4.707 2.054 2.540 4.965 3.084 3.028 4.749  
CYS325 SG3195 4.543 2.393 2.337 4.686 3.084 2.753 4.551  
CYS326 SG3203 4.389 2.877 2.393 4.463 3.150 2.555 4.391  
MET343 SD3358 2.251 3.448 2.410 2.341 2.412 1.568 2.286  
HIS112 MET162 MET177 MET184 CYS188 HIS191 HIS204  
NE21097 SD1621 SD1746 SD1807 SG1852 NE21878 NE22004  
MET162 SD1621 2.397  
MET177 SD1746 1.365 1.324  
MET184 SD1807 3.122 2.301 2.524  
CYS188 SG1852 3.341 3.278 3.249 1.268  
HIS191 NE21878 4.133 4.037 4.068 1.897 0.824  
HIS204 NE22004 3.488 2.492 2.973 0.744 1.316 1.786  
MET209 SD2046 3.356 2.724 2.723 0.735 1.484 1.994 1.396  
CYS220 SG2142 3.297 3.852 3.822 2.904 2.074 2.336 2.648  
HIS225 NE22193 4.112 4.239 4.434 3.027 2.162 2.147 2.583  
HIS256 NE22507 2.756 3.569 3.313 2.521 1.667 2.092 2.476  
MET259 SD2539 2.080 3.189 2.648 2.270 1.682 2.310 2.500  
CYS265 SG2593 3.478 3.955 3.795 2.313 1.119 1.217 2.232  
MET268 SD2619 3.001 3.830 3.620 2.841 1.956 2.285 2.724  
MET288 SD2813 1.725 1.083 0.430 2.658 3.501 4.312 3.072  
HIS290 NE22838 2.716 1.040 1.662 3.311 4.292 5.065 3.525  
HIS309 NE23045 3.761 2.717 3.565 4.182 4.675 5.280 3.896  
MET318 SD3122 5.133 3.725 4.806 4.221 4.571 4.896 3.633  
CYS325 SG3195 4.987 3.231 4.436 3.878 4.457 4.835 3.348  
CYS326 SG3203 4.846 2.786 4.082 3.701 4.506 4.955 3.290  
MET343 SD3358 2.644 0.554 1.460 2.747 3.783 4.541 2.978  
MET209 CYS220 HIS225 HIS256 MET259 CYS265 MET268  
SD2046 SG2142 NE22193 NE22507 SD2539 SG2593 SD2619  
CYS220 SG2142 3.388  
HIS225 NE22193 3.536 0.946  
HIS256 NE22507 2.891 0.819 1.597  
MET259 SD2539 2.492 1.732 2.482 0.938  
CYS265 SG2593 2.566 1.310 1.515 0.976 1.462  
MET268 SD2619 3.240 0.543 1.400 0.386 1.289 1.124  
MET288 SD2813 2.877 4.101 4.666 3.641 3.025 4.105 3.940  
HIS290 NE22838 3.660 4.727 5.173 4.446 4.013 4.924 4.692  
HIS309 NE23045 4.855 4.032 4.276 4.255 4.395 4.871 4.279  
MET318 SD3122 4.938 4.053 3.804 4.515 4.948 4.788 4.480  
CYS325 SG3195 4.559 4.320 4.119 4.649 4.942 4.872 4.687  
CYS326 SG3203 4.319 4.690 4.577 4.879 5.014 5.088 4.983  
MET343 SD3358 3.094 4.395 4.792 4.096 3.667 4.487 4.361  
MET288 HIS290 HIS309 MET318 CYS325 CYS326  
SD2813 NE22838 NE23045 SD3122 SG3195 SG3203  
HIS290 NE22838 1.264  
HIS309 NE23045 3.432 2.803  
MET318 SD3122 4.704 4.191 2.115  
CYS325 SG3195 4.276 3.659 2.127 0.879  
CYS326 SG3203 3.855 3.108 2.282 1.750 0.884  
MET343 SD3358 1.087 0.593 2.900 4.030 3.472 2.923  
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  
4  
Start terminus MET-1: 5TER  
Select end terminus type for THR-345  
0: COO-  
1: COOH  
2: CT2  
3: CT1  
4: HYD2  
5: MET2  
6: 3TER  
7: None  
6  
End terminus THR-345: 3TER

* * *

Program: gmx pdb2gmx, version 2023.3-conda\_forge  
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1115)

Fatal error:  
atom O5’ not found in buiding block 1MET while combining tdb and rtp