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