GROMACS version:
GROMACS modification: No
I am trying to run a calculation on water molecule but I am getting a Fatal error:
“Atom H1 in residue HOH 1 was not found in rtp entry HOH with 3 atoms while sorting atoms.”
Please help to overcome this error
The topology of the water molecule in your force field has no atom named “H1”. I guess it has an atom names “HW1”. If guess that if you replace "H1 " by “HW1” and "H2 " by “HW2” in your input it should work.
Is there any command to replace atom’s names directly according to columns ??
You can make replacements easily from the command line with sed. Just make sure not to shift any of the columns in the .pdb file.