Protein-heme-ligand simulation

abanishbiswas · June 6, 2024, 6:13am

GROMACS version:2022
GROMACS modification: Yes/No
Here post your question
I am trying to run MD simulation of protein-ligand complex. My protein is cyp1b1(PDB ID: 3PM0). While generating topology for protein it shows error due to heme. I tried to generate itp file for heme in swissparam, cgenff. But I could not run the simulation. Please provide me some solution to run the simulation.

Karis · June 6, 2024, 8:00am

Could you share the commands you used along with copy-pasting the outputs from the commands (notes, warnings, errors, etc)?

abanishbiswas · June 6, 2024, 11:17am

I tried -missing command and it worked with charm22 force field. I had to make some changes in .mdp and .top files.
“gmx pdb2gmx -f REC.pdb -ignh -missing”

Karis · June 6, 2024, 11:59am

I wouldn’t advise using the -missing flag, that just means you’re progressing with the simulation even if an atom is missing which could lead to nonsensical results later on (see this post, which also involves errors regarding heme so you might find it useful).

If the issue is with atoms missing from a protein, you could also take a look at this server that was designed for fixing such issues with pdb files

abanishbiswas · June 10, 2024, 10:24am

(base) bit@bit-HP-Z6-G4-Workstation:~/Desktop/RES$ source /usr/local/gromacs/bin/GMXRC
(base) bit@bit-HP-Z6-G4-Workstation:~/Desktop/RES$ gmx pdb2gmx -f REC.pdb -ignh
:-) GROMACS - gmx pdb2gmx, 2022.6 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/bit/Desktop/RES
Command line:
gmx pdb2gmx -f REC.pdb -ignh

Select the Force Field:

From ‘/usr/local/gromacs/share/gromacs/top’:

1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)

3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)

4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)

5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)

6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)

8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)

9: GROMOS96 43a1 force field

10: GROMOS96 43a2 force field (improved alkane dihedrals)

11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)

12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)

13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)

15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
8

Using the Charmm27 force field in directory charmm27.ff
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/watermodels.dat

Select the Water Model:

1: TIP3P TIP 3-point, recommended

2: TIP4P TIP 4-point

3: TIPS3P CHARMM TIP 3-point with LJ on H’s

4: TIP5P TIP 5-point (see OPLS/AA not compatible with TIP5P - Redmine #1348 (#1348) · Issues · GROMACS / GROMACS · GitLab for issues)

5: SPC simple point charge

6: SPC/E extended simple point charge

7: None
1

going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b

going to rename charmm27.ff/rna.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading REC.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 3723 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 2 chains and 0 blocks of water and 464 residues with 3723 atoms

chain #res #atoms

1 ‘A’ 463 3680

2 ‘A’ 1 43

All occupancies are one

All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp

Reading residue database… (Charmm27)
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Processing chain 1 ‘A’ (3680 atoms, 463 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 723 donors and 658 acceptors were found.
There are 950 hydrogen bonds
Will use HISE for residue 4
Will use HISE for residue 37
Will use HISE for residue 69
Will use HISE for residue 73
Will use HISE for residue 82
Will use HISE for residue 102
Will use HISE for residue 149
Will use HISE for residue 160
Will use HISH for residue 212
Will use HISE for residue 242
Will use HISD for residue 334
Will use HISE for residue 346
Will use HISE for residue 362
Will use HISE for residue 422

Identified residue GLN1 as a starting terminus.

Identified residue ASP463 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS4 CYS25 HIS37 MET65 HIS69 HIS73 HIS82
NE225 SG197 NE2287 SD495 NE2524 NE2561 NE2642
CYS25 SG197 2.119
HIS37 NE2287 2.393 2.724
MET65 SD495 2.476 2.242 2.109
HIS69 NE2524 2.590 1.205 2.594 1.346
HIS73 NE2561 3.730 2.601 3.060 1.490 1.416
HIS82 NE2642 2.593 2.888 1.710 0.909 2.164 2.151
MET84 SD657 3.414 3.565 2.930 1.348 2.595 2.103 1.225
MET85 SD665 2.687 3.117 2.453 1.032 2.338 2.285 0.816
HIS102 NE2814 3.400 4.213 3.593 2.294 3.493 3.365 2.052
MET138 SD1077 2.536 3.316 2.888 1.561 2.696 2.848 1.454
CYS142 SG1102 2.872 3.300 3.107 1.417 2.519 2.480 1.521
CYS145 SG1123 3.534 4.081 4.205 2.494 3.374 3.329 2.656
HIS149 NE21160 3.295 4.477 4.640 3.404 4.157 4.538 3.458
HIS160 NE21255 2.432 2.851 3.997 2.489 2.654 3.366 3.008
MET177 SD1379 1.972 1.083 3.452 2.909 2.056 3.454 3.535
HIS212 NE21697 3.730 3.946 3.950 2.092 3.041 2.693 2.283
CYS213 SG1705 4.040 3.763 4.039 2.006 2.705 2.062 2.424
MET225 SD1793 2.991 3.336 2.903 1.259 2.484 2.299 1.236
MET226 SD1801 3.457 3.459 3.594 1.617 2.504 2.157 1.965
HIS242 NE21916 5.087 4.803 3.658 2.781 3.710 2.578 2.514
CYS304 SG2397 3.562 4.920 3.454 3.161 4.424 4.449 2.494
MET305 SD2404 2.881 4.140 2.770 2.423 3.660 3.779 1.775
MET322 SD2540 1.565 3.046 1.977 2.008 2.896 3.491 1.610
HIS334 NE22637 1.656 1.550 1.454 1.147 1.337 2.228 1.434
HIS346 NE22723 2.937 1.602 2.234 2.780 2.017 2.910 3.123
HIS362 NE22856 0.806 2.741 2.119 2.683 3.079 4.050 2.516
MET394 SD3120 1.445 2.263 0.980 1.805 2.284 3.054 1.586
CYS403 SG3194 1.896 2.552 1.854 0.983 2.056 2.470 0.797
MET411 SD3254 2.855 3.840 2.587 1.953 3.241 3.256 1.321
HIS422 NE23345 3.488 5.156 4.014 3.725 4.848 5.110 3.206
CYS424 SG3362 2.984 4.703 4.095 3.585 4.522 4.983 3.287
MET436 SD3457 1.397 3.256 3.458 3.116 3.514 4.472 3.152
MET459 SD3643 3.659 5.210 4.665 3.903 4.898 5.198 3.630
MET84 MET85 HIS102 MET138 CYS142 CYS145 HIS149
SD657 SD665 NE2814 SD1077 SG1102 SG1123 NE21160
MET85 SD665 0.754
HIS102 NE2814 1.400 1.317
MET138 SD1077 1.271 0.736 0.924
CYS142 SG1102 0.953 0.721 0.998 0.559
CYS145 SG1123 1.872 1.843 1.132 1.361 1.144
HIS149 NE21160 3.106 2.753 1.966 2.025 2.223 1.551
HIS160 NE21255 2.888 2.472 2.599 2.029 2.008 1.914 1.908
MET177 SD1379 4.117 3.589 4.456 3.569 3.615 4.165 4.232
HIS212 NE21697 1.252 1.521 1.203 1.399 0.924 0.838 2.365
CYS213 SG1705 1.400 1.852 2.036 2.017 1.459 1.654 3.161
MET225 SD1793 0.575 0.461 1.086 0.731 0.403 1.471 2.583
MET226 SD1801 1.039 1.284 1.496 1.353 0.796 1.214 2.637
HIS242 NE21916 2.054 2.653 3.206 3.282 3.004 3.759 5.093
CYS304 SG2397 2.500 2.205 1.647 1.953 2.360 2.689 2.742
MET305 SD2404 1.985 1.535 1.403 1.345 1.805 2.399 2.597
MET322 SD2540 2.394 1.663 2.227 1.531 2.017 2.808 2.796
HIS334 NE22637 2.391 1.843 3.046 2.167 2.269 3.285 3.776
HIS346 NE22723 4.066 3.691 4.966 4.111 4.129 5.131 5.655
HIS362 NE22856 3.446 2.700 3.346 2.568 3.002 3.721 3.427
MET394 SD3120 2.731 2.083 3.127 2.308 2.602 3.601 3.835
CYS403 SG3194 1.567 0.849 1.925 1.082 1.328 2.370 2.893
MET411 SD3254 1.447 1.022 1.163 1.005 1.376 2.145 2.652
HIS422 NE23345 3.251 2.830 2.117 2.335 2.811 2.856 2.289
CYS424 SG3362 3.338 2.820 2.175 2.174 2.649 2.542 1.552
MET436 SD3457 3.613 2.907 3.044 2.411 2.829 3.063 2.260
MET459 SD3643 3.413 3.042 2.073 2.369 2.741 2.344 1.350
HIS160 MET177 HIS212 CYS213 MET225 MET226 HIS242
NE21255 SD1379 NE21697 SG1705 SD1793 SD1801 NE21916
MET177 SD1379 2.537
HIS212 NE21697 2.331 4.236
CYS213 SG1705 2.645 4.186 0.911
MET225 SD1793 2.368 3.762 1.063 1.458
MET226 SD1801 2.198 3.826 0.557 0.671 0.872
HIS242 NE21916 4.862 5.633 2.990 2.694 2.626 2.814
CYS304 SG2397 3.726 5.166 2.831 3.584 2.311 3.028 3.812
MET305 SD2404 3.182 4.428 2.470 3.140 1.739 2.540 3.491
MET322 SD2540 2.684 3.264 2.920 3.411 2.028 2.771 4.026
HIS334 NE22637 2.706 2.238 3.088 3.102 2.197 2.655 3.686
HIS346 NE22723 4.271 2.532 4.833 4.586 4.016 4.322 4.714
HIS362 NE22856 2.974 2.745 3.907 4.309 3.063 3.689 5.017
MET394 SD3120 3.148 2.758 3.508 3.712 2.516 3.177 3.990
CYS403 SG3194 2.368 2.993 2.236 2.528 1.254 1.945 3.246
MET411 SD3254 2.987 4.213 2.066 2.656 1.238 2.074 3.026
HIS422 NE23345 3.604 5.177 3.279 4.124 2.907 3.519 4.816
CYS424 SG3362 2.869 4.547 3.138 3.977 2.865 3.345 5.174
MET436 SD3457 2.080 2.850 3.552 4.111 3.077 3.476 5.542
MET459 SD3643 3.070 5.068 3.002 3.897 2.974 3.328 5.205
CYS304 MET305 MET322 HIS334 HIS346 HIS362 MET394
SG2397 SD2404 SD2540 NE22637 NE22723 NE22856 SD3120
MET305 SD2404 0.787
MET322 SD2540 2.061 1.355
HIS334 NE22637 3.511 2.724 1.740
HIS346 NE22723 5.364 4.592 3.546 1.964
HIS362 NE22856 3.138 2.514 1.201 1.892 3.222
MET394 SD3120 3.122 2.378 1.238 0.948 2.373 1.254
CYS403 SG3194 2.409 1.627 1.036 1.164 3.108 1.901 1.278
MET411 SD3254 1.212 0.547 1.400 2.420 4.294 2.600 2.240
HIS422 NE23345 1.085 1.474 2.258 3.911 5.793 3.078 3.472
CYS424 SG3362 1.842 1.863 2.138 3.686 5.569 2.747 3.356
MET436 SD3457 3.165 2.688 1.801 2.725 4.292 1.548 2.498
MET459 SD3643 1.952 2.161 2.748 4.199 6.133 3.482 3.970
CYS403 MET411 HIS422 CYS424 MET436
SG3194 SD3254 NE23345 SG3362 SD3457
MET411 SD3254 1.290
HIS422 NE23345 2.866 1.959
CYS424 SG3362 2.741 2.223 0.996
MET436 SD3457 2.370 2.822 2.708 1.929
MET459 SD3643 3.166 2.466 1.170 0.790 2.585
Start terminus GLN-1: NH3+
End terminus ASP-463: COO-
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 463 residues with 7318 atoms
Chain time…

Making bonds…

Number of bonds was 7409, now 7409

Generating angles, dihedrals and pairs…
Before cleaning: 19358 pairs
Before cleaning: 19583 dihedrals

Making cmap torsions…

There are 461 cmap torsion pairs

There are 19583 dihedrals, 1249 impropers, 13350 angles
19217 pairs, 7409 bonds and 0 virtual sites

Total mass 52220.004 a.m.u.

Total charge 5.000 e

Writing topology

Processing chain 2 ‘A’ (43 atoms, 1 residues)

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
Special Atom Distance matrix:
HEM464 HEM464
CAB20 CAC27
HEM464 CAC27 0.781
HEM464 FE43 0.556 0.549
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 1 residues with 43 atoms
Chain time…

Making bonds…

atom HA is missing in residue HEM 464 in the pdb file

You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HB is missing in residue HEM 464 in the pdb file

You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HC is missing in residue HEM 464 in the pdb file

You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HD is missing in residue HEM 464 in the pdb file

You might need to add atom HD to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMA1 is missing in residue HEM 464 in the pdb file

You might need to add atom HMA1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMA2 is missing in residue HEM 464 in the pdb file

You might need to add atom HMA2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMA3 is missing in residue HEM 464 in the pdb file

You might need to add atom HMA3 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAA1 is missing in residue HEM 464 in the pdb file

You might need to add atom HAA1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAA2 is missing in residue HEM 464 in the pdb file

You might need to add atom HAA2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBA1 is missing in residue HEM 464 in the pdb file

You might need to add atom HBA1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBA2 is missing in residue HEM 464 in the pdb file

You might need to add atom HBA2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMB1 is missing in residue HEM 464 in the pdb file

You might need to add atom HMB1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMB2 is missing in residue HEM 464 in the pdb file

You might need to add atom HMB2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMB3 is missing in residue HEM 464 in the pdb file

You might need to add atom HMB3 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAB is missing in residue HEM 464 in the pdb file

You might need to add atom HAB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBB1 is missing in residue HEM 464 in the pdb file

You might need to add atom HBB1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBB2 is missing in residue HEM 464 in the pdb file

You might need to add atom HBB2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMC1 is missing in residue HEM 464 in the pdb file

You might need to add atom HMC1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMC2 is missing in residue HEM 464 in the pdb file

You might need to add atom HMC2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMC3 is missing in residue HEM 464 in the pdb file

You might need to add atom HMC3 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAC is missing in residue HEM 464 in the pdb file

You might need to add atom HAC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBC1 is missing in residue HEM 464 in the pdb file

You might need to add atom HBC1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBC2 is missing in residue HEM 464 in the pdb file

You might need to add atom HBC2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMD1 is missing in residue HEM 464 in the pdb file

You might need to add atom HMD1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMD2 is missing in residue HEM 464 in the pdb file

You might need to add atom HMD2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HMD3 is missing in residue HEM 464 in the pdb file

You might need to add atom HMD3 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAD1 is missing in residue HEM 464 in the pdb file

You might need to add atom HAD1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HAD2 is missing in residue HEM 464 in the pdb file

You might need to add atom HAD2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBD1 is missing in residue HEM 464 in the pdb file

You might need to add atom HBD1 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

atom HBD2 is missing in residue HEM 464 in the pdb file

You might need to add atom HBD2 to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual)

Program: gmx pdb2gmx, version 2022.6
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1584)

Fatal error:
There were 30 missing atoms in molecule Other_chain_A2, if you want to use
this incomplete topology anyhow, use the option -missing

Karis · June 10, 2024, 10:47am

Have you tried running the pdb 3PM0 through the server I’d linked above before running the pdb2gmx command? If you follow the link in the abstract, it should take you to a website where you can submit the pdb, one of the functions is adding hydrogen atoms

abanishbiswas · June 10, 2024, 10:53am

I shall try the server and let you know.

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