Fatal Error in Gromacs

Question

[mahafujulislamtonmoy]

Recently I used HOXB13 protein for MD simulation by Gromacs. When I run OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) I got a fetal error and that Atom HA3 in residue GLY 1 was not found in rtp entry GLY with 9 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.

Please help me and what will be the command if i want to remove H atom from pdb file.

Thanks in advance.

[manaswwm]

What this error means is there is no HA3 entry in the residual topology (.rtp) file for GLY residue in OPLS FF (Force Field). I would suggest you to see the the .rtp file of OPLS FF and search what is the naming scheme there along with charge and rename your HA3 accordingly (as long as you know what HA3 represents). In my observation this usually happens when you switch from one FF to other for same molecule, the naming schemes change (for example naming scheme for CHARMM and OPLS are different and this is very visible when you compare their rtp files).

Answer 1

[safaa_kishk]

I have this message on GROMACS Fatal error: Atom HB3 in residue ASN 146 was not found in rtp entry ASN with 16 atoms while sorting atoms. Can anyone help how to solve it? Please support me with the commands that I should write on Linux. Thanks

[manaswwm]

As I have mentioned above, this very possibly means that whichever FF you are using, the .rtp entry of that FF does not recognize HB3 hydrogen atom for ASN residue. Kindly look at the .rtp file of the FF that you are using here. You will have to investigate the corresponding entry to HB3 in your FF and rename it accordingly in your structure file, this is not possible with commands on Linux, you will need to investigate and make changes manually.