Warnings in Gromacs

User discussions
1

GROMACS version: 2022
#warning:warning

When I am using pdb2gmx on my protein structure (antigen and antibody docked structure) , it throw some warnings. What does those warning mean? how to deal with them? can we ignore those warnings?

please find them below

$ gmx pdb2gmx -f test_clean.pdb -o test.gro -water tip3p -ignh -merge all -chainsep interactive -ff charmm36-mar2019 -his

`


INFO:Setting up molecule.
INFO:Created biomolecule object with 783 residues and 6097 atoms.
INFO:Setting termini states for biomolecule chains.
WARNING:Gap in backbone detected between LYS A 61 and SER A 62!
WARNING:Gap in backbone detected between SER A 62 and THR A 63!
WARNING:Gap in backbone detected between GLY A 219 and LYS A 220!
WARNING:Gap in backbone detected between LYS A 220 and LEU A 221!
WARNING:Gap in backbone detected between LEU A 221 and SER A 222!
WARNING:Gap in backbone detected between LEU A 277 and GLU A 278!
WARNING:Gap in backbone detected between ALA H 1 and VAL H 2!
WARNING:Gap in backbone detected between PRO H 41 and SER H 42!
WARNING:Gap in backbone detected between ARG H 44 and LEU H 45!
WARNING:Gap in backbone detected between ASP H 55 and ASP H 56!
WARNING:Gap in backbone detected between ASP H 56 and GLY H 57!
INFO:Loading forcefield.
INFO:Loading hydrogen topology definitions.
WARNING:Missing atom OXT in residue PRO A 663
WARNING:Missing atom OXT in residue GLU H 120
WARNING:Missing atom OXT in residue PRO A 663
WARNING:Missing atom OXT in residue GLU H 120
INFO:Attempting to repair 2 missing atoms in biomolecule.
WARNING:Missing atom OXT in residue PRO A 663
WARNING:Missing atom OXT in residue GLU H 120
INFO:Added atom OXT to residue PRO A 663 at coordinates 9.932, 0.740, 8.985
INFO:Added atom OXT to residue GLU H 120 at coordinates -37.035, -28.661, 6.102
INFO:Updating disulfide bridges.
INFO:Debumping biomolecule.
INFO:Adding hydrogens to biomolecule.
INFO:Debumping biomolecule (again).
WARNING:WARNING: Unable to debump MET A 343
WARNING:WARNING: Unable to debump PRO A 371
WARNING:WARNING: Unable to debump ASN A 373
WARNING:WARNING: Unable to debump GLY A 375
WARNING:WARNING: Unable to debump LYS A 377
WARNING:WARNING: Unable to debump GLU A 378
WARNING:WARNING: Unable to debump GLN A 397
WARNING:WARNING: Unable to debump GLU H 108
WARNING:WARNING: Unable to debump ALA H 109
WARNING:WARNING: Unable to debump TRP H 115
INFO:Optimizing hydrogen bonds
INFO:Applying force field to biomolecule states.
INFO:Regenerating headers.
INFO:Regenerating PDB lines.
WARNING:Ignoring 393 header lines in output.

Thanks

2

Hi,
it seems that some atoms missing in your pdb file or something is wrong in the pdb structure. You can visualize the pdb to better understand the source of your warning.

I saw that you use the options -merge all -chainsep interactive . If you do not specifically need them, I suggest to first run without these options to better understand the source of warnings.

\Alessandra

3

Hi,
Thanks for the suggestion.
using just gmx pdb2gmx -f test_clean.pdb -o test.gro -water tip3p shows no error. Everything seems fine with the structure. I am wondering why is it throwing errors while using additional options?

4

Hi,

In general, the combination of more options can make things more complicated and make more difficult to understand where the problem is. Some option and combination of option are not so trivial for the program. Thus it is why I suggested to start with the minimum options one need. Then increase the complexity if needed.

For example I have noticed that you have omitted -ff charmm36-mar2019. I guess that you provide the force filed charmm36-mar2019 from the command line. If it works, adding the opition -ff should be not problem. You omitted the option -his, is the assignment of his-protonation state the expected one ? Then you do not need -his.

\Alessandra

5

Thank you so much.
One more query,
should I assign protonation state of “HIS” ie ND or NE by converting pdb into pqr and seeing the protonation position in pqr file or Gromacs is enough intelligent to assign protonation of HIS based on the applied force field?

Thanks

6

Hi,
I do not have an answer to your question since it depends to your problem and to how hydrogen position is generate in your pqr file. I hope the points below help you to decide .

gmx pdb2gmx assigns the proton position of histidine based on an optimal hydrogen bonding conformation (hydrogen bonds are defined based on a simple geometric criterion, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance) . Information on the selected type can be found in standard output and topol file.

If you want to assign a different proton position, you can do manually using the option -his.

If you have hydrogen position in the experimental structure, dis-activate the option -ignh (ignore hydrogen atoms that are in the coordinate file)

\Alessandra

7

Thank you so much for the detailed explanation. It helped me in understanding the pdb2gmx function.