Please how can i neutralize the system?

User discussions
1

GROMACS version:2021
GROMACS modification: No
Here post your question

hello, i ve got this problem during Md run; please how can i neutralize the system?
when i add NA it will be 0.66000.

*NOTE 2 [file [topol.top](http://topol.top/), line 56]:*
*System has non-zero total charge: -0.340000*
*Total charge should normally be an integer. See*
*http://www.gromacs.org/Documentation/Floating_Point_Arithmetic*
*for discussion on how close it should be to an integer.*

*WARNING 1 [file [topol.top](http://topol.top/), line 56]:*
*You are using Ewald electrostatics in a system with net charge. This can*
*lead to severe artifacts, such as ions moving into regions with low*
*dielectric, due to the uniform background charge. We suggest to*
*neutralize your system with counter ions, possibly in combination with a*
*physiological salt concentration.*

I can pass this problem using -maxwarn in command line
or to change this line in mdp files:
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
to
coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics

Is it normal to use those solutions during MD? if not what is the solution to avoid the error?

2

A fractional charge of that magnitude means your topology is broken. -0.34 net charge is impossible.

1 Like
3

how can i fix it?

4

You need to tell us what you’ve done and what is in your system. Provide your entire pdb2gmx command and the full screen output from it.

1 Like
5

Thank you for your response.
I have used this lines; and my solvent system is water

gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

1
1840×306 46.4 KB

gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

2
2796×135 19.5 KB

we have used the file of solvant ions from Protein-Ligand Complex

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

3
3655×598 64.6 KB

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

4
4759×723 125 KB

and for Energy Minimization

we have used the file of solvent ions from open this: http://www.mdtutorials.com/gmx/complex/Files/em.mdp

gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

this shows the error mentioned in the topic

6

The problem comes from pdb2gmx but you did not provide that information. That is where the problem is. We need the full command and screen output (copy and paste is better than screenshots).

7

I have this command:

gmx pdb2gmx -f 5fsa6139_clean.pdb -o 5fsa6139_processed.gro

gmx pdb2gmx -f 5fsah_clean.pdb -o 5fsah_processed.gro

Select the Force Field:
From current directory:
1: CHARMM36 all-atom force field (July 2020)
From ‘/usr/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, 461-469, 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, 2006)
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: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Charmm36-feb2021 force field in directory ./charmm36-feb2021.ff

Opening force field file ./charmm36-feb2021.ff/watermodels.dat

Select the Water Model:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
2: TIP4P TIP 4-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
1
going to rename ./charmm36-feb2021.ff/merged.r2b
Opening force field file ./charmm36-feb2021.ff/merged.r2b
Reading 5fsah_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 4833 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 485 residues with 4833 atoms

chain #res #atoms
1 ‘A’ 484 4790
2 ’ ’ 1 43

WARNING: there were 4 atoms with zero occupancy and 34 atoms with
occupancy unequal to one (out of 4833 atoms). Check your pdb file.

Opening force field file ./charmm36-feb2021.ff/atomtypes.atp
Reading residue database… (Charmm36-feb2021)
Opening force field file ./charmm36-feb2021.ff/merged.rtp
Opening force field file ./charmm36-feb2021.ff/merged.hdb
Opening force field file ./charmm36-feb2021.ff/merged.n.tdb
Opening force field file ./charmm36-feb2021.ff/merged.c.tdb
Processing chain 1 ‘A’ (4790 atoms, 484 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 741 donors and 722 acceptors were found.
There are 956 hydrogen bonds
Will use HISE for residue 101
Will use HISE for residue 120
Will use HISE for residue 183
Will use HISE for residue 242
Will use HISE for residue 283
Will use HISE for residue 310
Will use HISE for residue 322
Will use HISE for residue 328
Will use HISE for residue 373
Will use HISE for residue 377
Will use HISE for residue 400
Will use HISE for residue 410
Will use HISE for residue 468
Identified residue LYS45 as a starting terminus.
Identified residue PHE528 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS75 MET86 MET92 HIS101 HIS120 CYS134 MET140
SG310 SD428 SD482 NE2565 NE2751 SG872 SD932
MET86 SD428 1.393
MET92 SD482 1.275 0.978
HIS101 NE2565 1.617 2.461 1.626
HIS120 NE2751 2.804 1.962 1.549 2.751
CYS134 SG872 3.417 3.052 2.266 2.599 1.448
MET140 SD932 3.160 3.184 2.267 1.966 2.149 1.036
HIS183 NE21394 4.841 5.294 4.811 4.537 4.983 5.035 5.130
MET189 SD1441 2.805 3.092 2.521 2.538 2.776 2.995 3.118
MET209 SD1633 4.710 4.555 3.805 3.842 2.988 2.323 2.826
HIS242 NE21971 3.071 2.596 2.227 3.090 1.650 2.370 2.984
MET258 SD2149 4.631 4.160 3.503 3.913 2.295 1.679 2.528
HIS283 NE22415 4.741 4.771 3.855 3.411 3.307 1.915 1.797
MET292 SD2503 4.112 3.867 3.039 3.084 2.206 0.872 1.365
MET306 SD2628 3.288 3.073 2.375 2.733 1.763 1.682 2.211
HIS310 NE22663 2.917 2.882 2.181 2.425 1.957 2.017 2.341
HIS322 NE22776 2.430 3.303 2.689 2.005 3.528 3.578 3.297
HIS328 NE22833 3.806 4.869 4.212 3.091 5.040 4.785 4.312
MET372 SD3268 2.230 3.229 2.594 1.720 3.566 3.575 3.190
HIS373 NE23281 2.217 3.041 2.399 1.772 3.237 3.305 3.039
MET374 SD3290 1.898 2.572 1.684 0.776 2.524 2.353 1.910
HIS377 NE23319 1.495 1.796 1.101 1.460 1.974 2.418 2.384
HIS400 NE23554 1.577 0.998 0.966 2.124 1.967 2.687 2.624
HIS410 NE23646 1.936 2.815 1.967 0.629 2.939 2.706 2.121
HIS468 NE24198 2.583 2.544 1.629 1.611 1.693 1.060 0.641
CYS470 SG4223 2.816 3.157 2.197 1.549 2.390 1.693 1.286
MET508 SD4594 2.306 2.165 1.455 2.015 1.443 1.822 2.111
CYS526 SG4769 5.803 6.354 5.672 5.038 5.738 5.351 5.308
MET527 SD4777 5.053 5.597 4.857 4.183 4.933 4.477 4.392
HIS183 MET189 MET209 HIS242 MET258 HIS283 MET292
NE21394 SD1441 SD1633 NE21971 SD2149 NE22415 SD2503
MET189 SD1441 2.312
MET209 SD1633 3.661 2.624
HIS242 NE21971 3.516 1.601 2.401
MET258 SD2149 4.654 3.155 1.237 2.313
HIS283 NE22415 5.075 3.669 2.069 3.631 2.114
MET292 SD2503 4.943 3.191 1.795 2.730 1.294 1.167
MET306 SD2628 3.469 1.581 1.510 1.099 1.614 2.566 1.800
HIS310 NE22663 3.107 1.043 1.893 1.082 2.173 2.865 2.213
HIS322 NE22776 2.673 1.349 3.584 2.796 4.158 4.050 3.813
HIS328 NE22833 2.781 2.714 4.412 4.280 5.248 4.665 4.811
MET372 SD3268 3.063 1.679 3.795 3.017 4.309 4.056 3.847
HIS373 NE23281 2.839 1.231 3.439 2.578 3.942 3.869 3.577
MET374 SD3290 3.829 1.813 3.187 2.513 3.402 3.081 2.733
HIS377 NE23319 3.730 1.471 3.252 1.776 3.308 3.625 2.966
HIS400 NE23554 5.768 3.486 4.580 3.055 4.098 4.359 3.532
HIS410 NE23646 3.975 2.124 3.540 2.958 3.803 3.279 3.055
HIS468 NE24198 4.969 2.809 2.970 2.601 2.636 2.344 1.693
CYS470 SG4223 3.895 2.011 2.356 2.446 2.595 2.064 1.818
MET508 SD4594 3.651 1.376 2.475 1.091 2.446 3.090 2.298
CYS526 SG4769 1.703 3.287 3.652 4.488 4.854 4.752 5.006
MET527 SD4777 1.752 2.598 2.947 3.816 4.118 3.906 4.149
MET306 HIS310 HIS322 HIS328 MET372 HIS373 MET374
SD2628 NE22663 NE22776 NE22833 SD3268 NE23281 SD3290
HIS310 NE22663 0.565
HIS322 NE22776 2.624 2.081
HIS328 NE22833 3.903 3.426 1.637
MET372 SD3268 2.807 2.283 0.413 1.642
HIS373 NE23281 2.402 1.863 0.302 1.897 0.455
MET374 SD3290 2.089 1.725 1.478 2.720 1.318 1.212
HIS377 NE23319 1.836 1.425 1.664 3.251 1.664 1.372 1.050
HIS400 NE23554 3.215 3.100 3.546 4.993 3.388 3.265 2.452
HIS410 NE23646 2.525 2.153 1.478 2.515 1.209 1.268 0.458
HIS468 NE24198 2.024 2.076 3.006 4.205 2.898 2.724 1.584
CYS470 SG4223 1.614 1.488 2.122 3.121 2.084 1.895 1.033
MET508 SD4594 0.992 0.736 2.141 3.650 2.247 1.866 1.463
CYS526 SG4769 4.030 3.790 3.437 2.925 3.738 3.605 4.348
MET527 SD4777 3.243 3.003 2.748 2.444 3.027 2.875 3.490
HIS377 HIS400 HIS410 HIS468 CYS470 MET508 CYS526
NE23319 NE23554 NE23646 NE24198 SG4223 SD4594 SG4769
HIS400 NE23554 2.048
HIS410 NE23646 1.410 2.634
HIS468 NE24198 1.862 2.028 1.854
CYS470 SG4223 1.693 2.927 1.304 1.268
MET508 SD4594 0.891 2.372 1.917 1.673 1.502
CYS526 SG4769 4.611 6.612 4.424 5.351 4.122 4.436
MET527 SD4777 3.826 5.782 3.577 4.447 3.210 3.636 0.921

Start terminus LYS-45: NH3+
End terminus PHE-528: COO-
Opening force field file ./charmm36-feb2021.ff/merged.arn

Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)

Fatal error:
Atom HN1 in residue LYS 45 was not found in rtp entry LYS with 24 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

Then I have used

-ignh -missing

to pass the error.

8

Never use -missing. Your topology is missing an N-terminal proton that leads to your problem. Use -ignh to have H atoms rebuilt and appropriately named to solve your issue.

1 Like
9

the new problem after using only -ignh

going to rename ./charmm36-feb2021.ff/merged.r2b
Opening force field file ./charmm36-feb2021.ff/merged.r2b
Reading 5fsah_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 3972 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 485 residues with 3972 atoms

chain #res #atoms
1 ‘A’ 484 3929
2 ’ ’ 1 43

WARNING: there were 4 atoms with zero occupancy and 34 atoms with
occupancy unequal to one (out of 3972 atoms). Check your pdb file.

Opening force field file ./charmm36-feb2021.ff/atomtypes.atp
Reading residue database… (Charmm36-feb2021)
Opening force field file ./charmm36-feb2021.ff/merged.rtp
Opening force field file ./charmm36-feb2021.ff/merged.hdb
Opening force field file ./charmm36-feb2021.ff/merged.n.tdb
Opening force field file ./charmm36-feb2021.ff/merged.c.tdb
Processing chain 1 ‘A’ (3929 atoms, 484 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 741 donors and 722 acceptors were found.
There are 956 hydrogen bonds
Will use HISE for residue 101
Will use HISE for residue 120
Will use HISE for residue 183
Will use HISE for residue 242
Will use HISE for residue 283
Will use HISE for residue 310
Will use HISE for residue 322
Will use HISE for residue 328
Will use HISE for residue 373
Will use HISE for residue 377
Will use HISE for residue 400
Will use HISE for residue 410
Will use HISE for residue 468
Identified residue LYS45 as a starting terminus.
Identified residue PHE528 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS75 MET86 MET92 HIS101 HIS120 CYS134 MET140
SG262 SD357 SD402 NE2471 NE2625 SG728 SD775
MET86 SD357 1.393
MET92 SD402 1.275 0.978
HIS101 NE2471 1.617 2.461 1.626
HIS120 NE2625 2.804 1.962 1.549 2.751
CYS134 SG728 3.417 3.052 2.266 2.599 1.448
MET140 SD775 3.160 3.184 2.267 1.966 2.149 1.036
HIS183 NE21148 4.841 5.294 4.811 4.537 4.983 5.035 5.130
MET189 SD1186 2.805 3.092 2.521 2.538 2.776 2.995 3.118
MET209 SD1344 4.710 4.555 3.805 3.842 2.988 2.323 2.826
HIS242 NE21624 3.071 2.596 2.227 3.090 1.650 2.370 2.984
MET258 SD1762 4.631 4.160 3.503 3.913 2.295 1.679 2.528
HIS283 NE21974 4.741 4.771 3.855 3.411 3.307 1.915 1.797
MET292 SD2043 4.112 3.867 3.039 3.084 2.206 0.872 1.365
MET306 SD2149 3.288 3.073 2.375 2.733 1.763 1.682 2.211
HIS310 NE22177 2.917 2.882 2.181 2.425 1.957 2.017 2.341
HIS322 NE22270 2.430 3.303 2.689 2.005 3.528 3.578 3.297
HIS328 NE22317 3.806 4.869 4.212 3.091 5.040 4.785 4.312
MET372 SD2673 2.230 3.229 2.594 1.720 3.566 3.575 3.190
HIS373 NE22684 2.217 3.041 2.399 1.772 3.237 3.305 3.039
MET374 SD2691 1.898 2.572 1.684 0.776 2.524 2.353 1.910
HIS377 NE22717 1.495 1.796 1.101 1.460 1.974 2.418 2.384
HIS400 NE22906 1.577 0.998 0.966 2.124 1.967 2.687 2.624
HIS410 NE22984 1.936 2.815 1.967 0.629 2.939 2.706 2.121
HIS468 NE23435 2.583 2.544 1.629 1.611 1.693 1.060 0.641
CYS470 SG3452 2.816 3.157 2.197 1.549 2.390 1.693 1.286
MET508 SD3762 2.306 2.165 1.455 2.015 1.443 1.822 2.111
CYS526 SG3910 5.803 6.354 5.672 5.038 5.738 5.351 5.308
MET527 SD3917 5.053 5.597 4.857 4.183 4.933 4.477 4.392
HIS183 MET189 MET209 HIS242 MET258 HIS283 MET292
NE21148 SD1186 SD1344 NE21624 SD1762 NE21974 SD2043
MET189 SD1186 2.312
MET209 SD1344 3.661 2.624
HIS242 NE21624 3.516 1.601 2.401
MET258 SD1762 4.654 3.155 1.237 2.313
HIS283 NE21974 5.075 3.669 2.069 3.631 2.114
MET292 SD2043 4.943 3.191 1.795 2.730 1.294 1.167
MET306 SD2149 3.469 1.581 1.510 1.099 1.614 2.566 1.800
HIS310 NE22177 3.107 1.043 1.893 1.082 2.173 2.865 2.213
HIS322 NE22270 2.673 1.349 3.584 2.796 4.158 4.050 3.813
HIS328 NE22317 2.781 2.714 4.412 4.280 5.248 4.665 4.811
MET372 SD2673 3.063 1.679 3.795 3.017 4.309 4.056 3.847
HIS373 NE22684 2.839 1.231 3.439 2.578 3.942 3.869 3.577
MET374 SD2691 3.829 1.813 3.187 2.513 3.402 3.081 2.733
HIS377 NE22717 3.730 1.471 3.252 1.776 3.308 3.625 2.966
HIS400 NE22906 5.768 3.486 4.580 3.055 4.098 4.359 3.532
HIS410 NE22984 3.975 2.124 3.540 2.958 3.803 3.279 3.055
HIS468 NE23435 4.969 2.809 2.970 2.601 2.636 2.344 1.693
CYS470 SG3452 3.895 2.011 2.356 2.446 2.595 2.064 1.818
MET508 SD3762 3.651 1.376 2.475 1.091 2.446 3.090 2.298
CYS526 SG3910 1.703 3.287 3.652 4.488 4.854 4.752 5.006
MET527 SD3917 1.752 2.598 2.947 3.816 4.118 3.906 4.149
MET306 HIS310 HIS322 HIS328 MET372 HIS373 MET374
SD2149 NE22177 NE22270 NE22317 SD2673 NE22684 SD2691
HIS310 NE22177 0.565
HIS322 NE22270 2.624 2.081
HIS328 NE22317 3.903 3.426 1.637
MET372 SD2673 2.807 2.283 0.413 1.642
HIS373 NE22684 2.402 1.863 0.302 1.897 0.455
MET374 SD2691 2.089 1.725 1.478 2.720 1.318 1.212
HIS377 NE22717 1.836 1.425 1.664 3.251 1.664 1.372 1.050
HIS400 NE22906 3.215 3.100 3.546 4.993 3.388 3.265 2.452
HIS410 NE22984 2.525 2.153 1.478 2.515 1.209 1.268 0.458
HIS468 NE23435 2.024 2.076 3.006 4.205 2.898 2.724 1.584
CYS470 SG3452 1.614 1.488 2.122 3.121 2.084 1.895 1.033
MET508 SD3762 0.992 0.736 2.141 3.650 2.247 1.866 1.463
CYS526 SG3910 4.030 3.790 3.437 2.925 3.738 3.605 4.348
MET527 SD3917 3.243 3.003 2.748 2.444 3.027 2.875 3.490
HIS377 HIS400 HIS410 HIS468 CYS470 MET508 CYS526
NE22717 NE22906 NE22984 NE23435 SG3452 SD3762 SG3910
HIS400 NE22906 2.048
HIS410 NE22984 1.410 2.634
HIS468 NE23435 1.862 2.028 1.854
CYS470 SG3452 1.693 2.927 1.304 1.268
MET508 SD3762 0.891 2.372 1.917 1.673 1.502
CYS526 SG3910 4.611 6.612 4.424 5.351 4.122 4.436
MET527 SD3917 3.826 5.782 3.577 4.447 3.210 3.636 0.921

Start terminus LYS-45: NH3+
End terminus PHE-528: COO-
Opening force field file ./charmm36-feb2021.ff/merged.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 484 residues with 7799 atoms
Chain time…
Making bonds…
Number of bonds was 7910, now 7910
Generating angles, dihedrals and pairs…
Before cleaning: 20814 pairs
Before cleaning: 21059 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 482 cmap torsion pairs
There are 21059 dihedrals, 1297 impropers, 14293 angles
20625 pairs, 7910 bonds and 0 virtual sites
Total mass 55608.682 a.m.u.
Total charge -1.000 e
Writing topology
Processing chain 2 (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:
HEME0 HEME0
CAB20 CAC27
HEME0 CAC27 0.689
HEME0 Fe43 1.007 0.632
Opening force field file ./charmm36-feb2021.ff/merged.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…
Warning: Long Bond (1-2 = 0.376383 nm)
Warning: Long Bond (1-4 = 0.717554 nm)
Warning: Long Bond (1-5 = 0.413299 nm)
Warning: Long Bond (2-6 = 0.511743 nm)
Warning: Long Bond (6-7 = 0.503469 nm)
Warning: Long Bond (7-8 = 0.431017 nm)
Warning: Long Bond (8-9 = 0.333521 nm)
Warning: Long Bond (7-27 = 0.809707 nm)
Warning: Long Bond (27-28 = 0.732382 nm)
Warning: Long Bond (28-29 = 0.717554 nm)
Warning: Long Bond (29-30 = 0.716079 nm)
Warning: Long Bond (29-31 = 0.316329 nm)
Warning: Long Bond (8-26 = 0.284035 nm)
Warning: Long Bond (23-9 = 0.299013 nm)
Warning: Long Bond (23-10 = 0.787275 nm)
Warning: Long Bond (3-10 = 0.948874 nm)
Warning: Long Bond (10-11 = 1.20847 nm)
Warning: Long Bond (11-12 = 1.13427 nm)
Warning: Long Bond (12-13 = 0.923594 nm)
Warning: Long Bond (3-13 = 0.460306 nm)
Warning: Long Bond (11-32 = 1.08176 nm)
Warning: Long Bond (12-33 = 0.337877 nm)
Warning: Long Bond (33-34 = 0.808382 nm)
Warning: Long Bond (24-13 = 0.642844 nm)
Warning: Long Bond (24-14 = 0.642262 nm)
Warning: Long Bond (4-14 = 0.522709 nm)
Warning: Long Bond (14-15 = 0.42877 nm)
Warning: Long Bond (15-16 = 0.293668 nm)
Warning: Long Bond (4-17 = 0.447375 nm)
Warning: Long Bond (15-35 = 0.466005 nm)
Warning: Long Bond (25-18 = 0.423339 nm)
Warning: Long Bond (18-19 = 0.510099 nm)
Warning: Long Bond (20-21 = 0.288529 nm)
Warning: Long Bond (19-38 = 0.447402 nm)
Warning: Long Bond (20-39 = 0.523604 nm)
Warning: Long Bond (39-40 = 0.434792 nm)
Warning: Long Bond (41-42 = 0.361641 nm)
Warning: Long Bond (41-43 = 0.30647 nm)
Warning: Long Bond (22-21 = 0.513304 nm)
Warning: Long Bond (22-6 = 0.763283 nm)

WARNING: atom HA is missing in residue HEME 0 in the pdb file
You might need to add atom HA to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HB is missing in residue HEME 0 in the pdb file
You might need to add atom HB to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HC is missing in residue HEME 0 in the pdb file
You might need to add atom HC to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HD is missing in residue HEME 0 in the pdb file
You might need to add atom HD to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMA1 is missing in residue HEME 0 in the pdb file
You might need to add atom HMA1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMA2 is missing in residue HEME 0 in the pdb file
You might need to add atom HMA2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMA3 is missing in residue HEME 0 in the pdb file
You might need to add atom HMA3 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAA1 is missing in residue HEME 0 in the pdb file
You might need to add atom HAA1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAA2 is missing in residue HEME 0 in the pdb file
You might need to add atom HAA2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBA1 is missing in residue HEME 0 in the pdb file
You might need to add atom HBA1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBA2 is missing in residue HEME 0 in the pdb file
You might need to add atom HBA2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMB1 is missing in residue HEME 0 in the pdb file
You might need to add atom HMB1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMB2 is missing in residue HEME 0 in the pdb file
You might need to add atom HMB2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMB3 is missing in residue HEME 0 in the pdb file
You might need to add atom HMB3 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAB is missing in residue HEME 0 in the pdb file
You might need to add atom HAB to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBB1 is missing in residue HEME 0 in the pdb file
You might need to add atom HBB1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBB2 is missing in residue HEME 0 in the pdb file
You might need to add atom HBB2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMC1 is missing in residue HEME 0 in the pdb file
You might need to add atom HMC1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMC2 is missing in residue HEME 0 in the pdb file
You might need to add atom HMC2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMC3 is missing in residue HEME 0 in the pdb file
You might need to add atom HMC3 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAC is missing in residue HEME 0 in the pdb file
You might need to add atom HAC to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBC1 is missing in residue HEME 0 in the pdb file
You might need to add atom HBC1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBC2 is missing in residue HEME 0 in the pdb file
You might need to add atom HBC2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMD1 is missing in residue HEME 0 in the pdb file
You might need to add atom HMD1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMD2 is missing in residue HEME 0 in the pdb file
You might need to add atom HMD2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HMD3 is missing in residue HEME 0 in the pdb file
You might need to add atom HMD3 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAD1 is missing in residue HEME 0 in the pdb file
You might need to add atom HAD1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HAD2 is missing in residue HEME 0 in the pdb file
You might need to add atom HAD2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBD1 is missing in residue HEME 0 in the pdb file
You might need to add atom HBD1 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

WARNING: atom HBD2 is missing in residue HEME 0 in the pdb file
You might need to add atom HBD2 to the hydrogen database of building block HEME
in the file merged.hdb (see the manual)

Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1494)

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

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

10

Long bonds mean your structure is incomplete or the coordinates are not correct. There is no .hdb entry for heme in the C36 port so either you need to fix the H nomenclature and not use -ignh or write the .hdb entry for heme yourself.

2 Likes
11

I have done both, and correct the PDB file, and it worked.
Thank you very much for you instructions; I appreciate your kind and important assistance.

Best regards.