Urgent help: System has non-zero total charge

User discussions
21

when i run gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -ter
first i got this error
Fatal error:
Atom HN1 in residue SER 45 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.

then i run the command as
gmx pdb2gmx -f pro.pdb -o pro_processed.gro -ter -ignh -missing
then i got this
End terminus ASN-496: COO-
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 452 residues with 7399 atoms
Chain time…
Making bonds…
Number of bonds was 7478, now 7478
Generating angles, dihedrals and pairs…
Before cleaning: 19655 pairs
Before cleaning: 19830 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 450 cmap torsion pairs
There are 19830 dihedrals, 1166 impropers, 13567 angles
19520 pairs, 7478 bonds and 0 virtual sites
Total mass 52147.359 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:
HEM600 HEM600
CAB2 CAC3
HEM600 CAC3 0.797
HEM600 FE43 0.562 0.566
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/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…

WARNING: atom HA is missing in residue HEM 600 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)

WARNING: atom HB is missing in residue HEM 600 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)

WARNING: atom HC is missing in residue HEM 600 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)

WARNING: atom HD is missing in residue HEM 600 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)

WARNING: atom HMA1 is missing in residue HEM 600 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)

WARNING: atom HMA2 is missing in residue HEM 600 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)

WARNING: atom HMA3 is missing in residue HEM 600 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)

WARNING: atom HAA1 is missing in residue HEM 600 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)

WARNING: atom HAA2 is missing in residue HEM 600 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)

WARNING: atom HBA1 is missing in residue HEM 600 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)

WARNING: atom HBA2 is missing in residue HEM 600 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)

WARNING: atom HMB1 is missing in residue HEM 600 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)

WARNING: atom HMB2 is missing in residue HEM 600 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)

WARNING: atom HMB3 is missing in residue HEM 600 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)

WARNING: atom HAB is missing in residue HEM 600 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)

WARNING: atom HBB1 is missing in residue HEM 600 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)

WARNING: atom HBB2 is missing in residue HEM 600 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)

WARNING: atom HMC1 is missing in residue HEM 600 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)

WARNING: atom HMC2 is missing in residue HEM 600 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)

WARNING: atom HMC3 is missing in residue HEM 600 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)

WARNING: atom HAC is missing in residue HEM 600 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)

WARNING: atom HBC1 is missing in residue HEM 600 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)

WARNING: atom HBC2 is missing in residue HEM 600 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)

WARNING: atom HMD1 is missing in residue HEM 600 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)

WARNING: atom HMD2 is missing in residue HEM 600 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)

WARNING: atom HMD3 is missing in residue HEM 600 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)

WARNING: atom HAD1 is missing in residue HEM 600 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)

WARNING: atom HAD2 is missing in residue HEM 600 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)

WARNING: atom HBD1 is missing in residue HEM 600 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)

WARNING: atom HBD2 is missing in residue HEM 600 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)

There were 30 missing atoms in molecule Other_chain_A2
Number of bonds was 50, now 50
Generating angles, dihedrals and pairs…
Before cleaning: 114 pairs

WARNING: WARNING: Residue 1 named HEM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HA used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named HEM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HB used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named HEM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HC used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 1 named HEM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HD used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

Before cleaning: 134 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 134 dihedrals, 46 impropers, 82 angles
102 pairs, 50 bonds and 0 virtual sites
Total mass 584.245 a.m.u.
Total charge -5.340 e
Writing topology
Including chain 1 in system: 7399 atoms 452 residues
Including chain 2 in system: 43 atoms 1 residues
Now there are 7442 atoms and 453 residues
Total mass in system 52731.604 a.m.u.
Total charge in system -0.340 e

Writing coordinate file…
--------- PLEASE NOTE ------------
You have successfully generated a topology from: pro.pdb.
The Charmm27 force field and the tip3p water model are used.
--------- ETON ESAELP ------------

GROMACS reminds you: “I am at two with nature.” (Woody Allen)

22

The problem is because you used the -missing option. You need -ignh to address the nomenclature issue but if you allow pdb2gmx to keep going when something is missing, it means you’ll get a nonsensical result. It is an option that one should basically never use.

23

what should i do then when i used only -ignh option it showed another error

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

24

Missing H atoms can be rebuilt with an appropriate entry in an .hdb file. One likely doesn’t exist for heme in the old version of the CHARMM force field that you’re trying to use. I strongly recommend using our CHARMM36 port, which is more comprehensive (and it is the latest version of the force field, not one that is over a decade old). See the third-party tools forum for the link.

25

thank you sir for helping.
i am beginner and don’t know well how i can use CHARMM36 forcefield as this option was not present when i run the command

26

If you download the CHARMM36 forcefield folder from the website and include it in your working directory, you can specify to use that forcefield by adding -ff charm36-jul2022 to your pdb2gmx command

27

Thank you so much will do it now

28

I have to download this .tgz file ?

IMG_20230715_211308.jpg
IMG_20230715_211308.jpg2304×1064 988 KB

29

i download the Charmm36-jul2022.ff.tgz files and extract the folder in my working directory, i gave the command as you told but it the system give me this responce
Inconsistency in user input:
Could not find force field ‘charm36-jul2022’ in current directory, install
tree or GMXLIB path.

30

Typo, should be -ff charmm36-jul2022 (or whatever the name of the folder is if you renamed it)

31

the folder name is charmm36-jul2022.ff. Should i write ff in the end ? as - charmm36-jul2022.ff

32

Don’t include the .ff in the command

33

okay so it will be – charmm36-jul2022?

34

it worked…it ask me to select the terminus
which option should i select
Select start terminus type for SER-45
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None

35

As Prof. Lemkul mentioned above, NH3+ and COO- are reasonable for neutral pH

36

i used these but again getting the same error

Fatal error:
Atom HN3 in residue SER 45 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.

37

using of -ignh option is not harmfull for the results. right ?

38

i used this option and i didn’t get any other error which i was getting last time… and i was using -missing command

39

@jalemkul @Karis thanks a lot for the help.
i didn’t get errors related to missing atoms or non-zero charge values. it solved my problems.
but when i run nvt.mdp file it showed a new error :(

Fatal error:
73 atoms are not part of any of the T-Coupling groups

there is note as well

NOTE 1 [file topol.top, line 56]:
The bond in molecule-type lig between atoms 18 C13 and 19 O15 has an
estimated oscillational period of 1.9e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.

40

The -ignh option is safe. pdb2gmx can rebuild H atoms with correct nomenclature and that is what is doing. The -missing option has very limited use and will build a bad topology because you’re telling it to. My basic advice is to never use it.