GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: Yes/No (don’t know what this means)
I am new to this so I don’t know what information you need to at all be able to try and answer my question. Please ask if something is missing.
I’ve been visualising an enzyme in VMD from a gro-file. The enzyme has the ions MG, NA and ZN around it.
It had 4 chains from the beginning and ions I didn’t want to keep. So I used:
gmx make_ndx -f .gro and got an index file.
I made a group with what I wanted to keep and in the following command I used this to make a new gro-file:
gmx trjconv -s md_nowater.tpr -f .gro -n index.ndx -o .pdb
Then I took this pdb file to go:
gmx pdb2gmx -f .pdb -o .gro -water tip3p
I come to the step where you should chose the force field and chose amber99sb-ildn. And I get the following, fatal, error:
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom HE2 in residue HIS 355 was not found in rtp entry HID with 17 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
I don’t know what this means or how to solve it.
I am following instructions from a supervisor but having said that, not everything has been correct so far as he hasn’t previously done these steps in his research himself.