# Protein-specific termini
**URL:** https://gromacs.bioexcel.eu/t/protein-specific-termini/7196
**Category:** User discussions
**Tags:** pdb2gmx
**Created:** [September 15, 2023, 5:16pm UTC](https://gromacs.bioexcel.eu/t/protein-specific-termini/7196 "2023-09-15T17:16:48Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Bisma](https://gromacs.bioexcel.eu/u/Bisma)
#### Post date: [September 15, 2023, 5:16pm UTC](https://gromacs.bioexcel.eu/t/protein-specific-termini/7196/1 "2023-09-15T17:16:48Z")
Hey i am following this tutorial on my protein : [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html)
But receiving following error :
Command line:
gmx pdb2gmx -f RIP1-IN-4\_Protein.pdb -o RIP1-IN-4\_Protein.gro -ter
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/share/apps/packages/gromacs/gromacs-5.1/build-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, 461-46 9, 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, 200 6)
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: 10.10 07/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
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)
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
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading RIP1-IN-4\_Protein.pdb…
Read 4925 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 308 residues with 4925 atoms
chain #res #atoms
1 ‘A’ 308 4925
All occupancies are one
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp
Atomtype 579
Reading residue database… (charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Residue 540
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Residue 903
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Residue 1826
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Residue 1850
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Residue 2261
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Residue 2268
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/na.rtp
Residue 2346
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Residue 2351
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Residue 2427
Sorting it all out…
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb
Processing chain 1 ‘A’ (4925 atoms, 308 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 449 donors and 466 acceptors were found.
There are 515 hydrogen bonds
Will use HISE for residue 36
Will use HISE for residue 56
Will use HISE for residue 72
Will use HISE for residue 102
Will use HISE for residue 130
Will use HISE for residue 136
Will use HISE for residue 151
Will use HISE for residue 173
Will use HISE for residue 197
Identified residue SER6 as a starting terminus.
Identified residue ALA313 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET12 CYS34 HIS36 MET42 MET44 CYS53 HIS56
SD110 SG423 NE2458 SD553 SD589 SG735 NE2784
CYS34 SG423 0.765
HIS36 NE2458 0.437 1.025
MET42 SD553 0.410 0.650 0.594
MET44 SD589 0.476 0.393 0.857 0.487
CYS53 SG735 2.110 1.961 2.507 2.297 1.831
HIS56 NE2784 2.205 1.853 2.627 2.253 1.808 0.791
MET66 SD937 2.344 2.358 2.711 2.251 2.142 2.294 1.939
MET67 SD954 1.540 1.507 1.903 1.398 1.308 2.017 1.693
HIS72 NE21055 2.645 2.738 2.837 2.398 2.577 3.521 3.147
MET92 SD1383 1.270 1.099 1.617 1.053 0.976 2.035 1.698
MET95 SD1436 1.758 1.613 1.911 1.386 1.608 3.004 2.610
MET101 SD1530 3.132 2.590 3.345 2.778 2.778 3.588 2.899
HIS102 NE21550 2.446 1.856 2.581 2.082 2.128 3.292 2.747
MET108 SD1646 3.438 3.045 3.449 3.031 3.258 4.650 4.113
MET126 SD1933 2.897 2.712 3.189 2.634 2.646 3.210 2.634
CYS127 SG1949 3.386 3.334 3.616 3.116 3.228 3.935 3.429
HIS130 NE22004 3.245 3.102 3.559 3.021 3.000 3.333 2.771
HIS136 NE22092 2.522 2.274 2.845 2.273 2.223 2.741 2.148
HIS151 NE22339 2.593 2.567 2.626 2.225 2.555 4.013 3.615
MET164 SD2544 2.381 2.108 2.816 2.394 2.009 1.132 0.555
HIS173 NE22698 4.398 3.862 4.793 4.264 3.946 3.235 2.524
MET193 SD3005 3.632 3.207 4.005 3.431 3.232 3.056 2.307
HIS197 NE23064 3.751 3.446 4.120 3.556 3.406 3.280 2.603
CYS233 SG3628 4.681 4.063 5.015 4.450 4.227 4.013 3.236
MET239 SD3727 5.090 4.559 5.430 4.843 4.668 4.498 3.721
CYS240 SG3743 4.852 4.303 5.172 4.583 4.433 4.418 3.630
CYS256 SG3986 4.174 3.806 4.352 3.801 3.908 4.767 4.082
MET264 SD4119 4.164 3.766 4.392 3.817 3.857 4.502 3.785
CYS267 SG4176 4.002 3.744 4.260 3.697 3.738 4.273 3.616
MET66 MET67 HIS72 MET92 MET95 MET101 HIS102
SD937 SD954 NE21055 SD1383 SD1436 SD1530 NE21550
MET67 SD954 0.877
HIS72 NE21055 1.468 1.533
MET92 SD1383 1.329 0.469 1.744
MET95 SD1436 1.850 1.212 1.383 0.980
MET101 SD1530 2.658 2.324 2.483 2.125 1.762
HIS102 NE21550 2.819 2.183 2.658 1.809 1.448 1.038
MET108 SD1646 3.680 3.159 2.918 2.861 2.045 1.630 1.448
MET126 SD1933 1.265 1.477 1.119 1.671 1.543 1.764 2.269
CYS127 SG1949 1.758 2.065 0.899 2.290 1.930 2.340 2.853
HIS130 NE22004 1.250 1.743 1.325 2.029 2.024 2.184 2.761
HIS136 NE22092 1.074 1.104 1.348 1.258 1.351 1.617 1.985
HIS151 NE22339 2.506 2.097 1.356 1.978 1.034 2.121 1.998
MET164 SD2544 1.509 1.496 2.826 1.640 2.524 2.820 2.832
HIS173 NE22698 3.117 3.308 4.037 3.371 3.814 2.839 3.422
MET193 SD3005 2.012 2.287 2.674 2.416 2.674 1.927 2.647
HIS197 NE23064 1.779 2.271 2.364 2.505 2.709 2.251 2.989
CYS233 SG3628 3.586 3.638 4.090 3.602 3.743 2.284 3.036
MET239 SD3727 3.608 3.843 3.977 3.896 3.943 2.556 3.487
CYS240 SG3743 3.506 3.657 3.770 3.671 3.645 2.168 3.114
CYS256 SG3986 3.190 3.141 2.500 3.092 2.470 1.482 2.326
MET264 SD4119 2.951 2.999 2.506 2.996 2.540 1.411 2.388
CYS267 SG4176 2.370 2.646 1.916 2.784 2.432 1.930 2.783
MET108 MET126 CYS127 HIS130 HIS136 HIS151 MET164
SD1646 SD1933 SG1949 NE22004 NE22092 NE22339 SD2544
MET126 SD1933 2.784
CYS127 SG1949 2.989 0.863
HIS130 NE22004 3.267 0.518 0.869
HIS136 NE22092 2.758 0.514 1.351 0.877
HIS151 NE22339 1.790 1.864 1.799 2.302 1.953
MET164 SD2544 4.108 2.267 3.037 2.327 1.823 3.470
HIS173 NE22698 4.462 2.971 3.706 2.919 2.730 4.518 2.347
MET193 SD3005 3.503 1.577 2.285 1.525 1.439 3.245 1.954
HIS197 NE23064 3.694 1.326 1.868 1.071 1.371 3.158 2.152
CYS233 SG3628 3.791 2.994 3.652 3.057 2.840 4.264 3.109
MET239 SD3727 4.011 2.876 3.362 2.816 2.881 4.302 3.463
CYS240 SG3743 3.589 2.685 3.183 2.698 2.682 3.979 3.401
CYS256 SG3986 1.925 1.940 1.972 2.199 2.186 2.209 3.849
MET264 SD4119 2.311 1.724 1.891 1.907 1.954 2.474 3.518
CYS267 SG4176 2.857 1.178 1.118 1.163 1.592 2.364 3.242
HIS173 MET193 HIS197 CYS233 MET239 CYS240 CYS256
NE22698 SD3005 NE23064 SG3628 SD3727 SG3743 SG3986
MET193 SD3005 1.422
HIS197 NE23064 1.948 0.671
CYS233 SG3628 1.250 1.650 2.216
MET239 SD3727 1.648 1.626 1.939 0.960
CYS240 SG3743 1.785 1.572 1.934 0.872 0.442
CYS256 SG3986 3.593 2.456 2.453 2.881 2.649 2.295
MET264 SD4119 3.080 1.957 1.965 2.414 2.121 1.791 0.567
CYS267 SG4176 3.144 1.804 1.496 2.828 2.404 2.210 1.246
MET264
SD4119
CYS267 SG4176 0.948
Select start terminus type for SER-6
0: NH3+
1: NH2
2: None
0
Start terminus SER-6: NH3+
Select end terminus type for ALA-313
0: COO-
1: COOH
2: CT2
3: CT1
4: None
0
End terminus ALA-313: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
* * *
Program gmx pdb2gmx, VERSION 5.1
Source code file: /share/apps/packages/gromacs/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746
Fatal error:
Atom HB3 in residue SER 6 was not found in rtp entry SER with 13 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
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)
Please help me as i am new to this kind of task
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 15, 2023, 8:08pm UTC](https://gromacs.bioexcel.eu/t/protein-specific-termini/7196/2 "2023-09-15T20:08:39Z")
Did you visit the link provided in the error message? It will lead you to the solution.
Please also note that version 5.1 of GROMACS is wildly outdated and not supported any more. You should upgrade to the latest version before doing anything else.