Change in protein conformation after addition of ions

GROMACS version:2019
GROMACS modification: No

I used the ions.mdp file provided in the gromacs tutorial to add ions to my protein ligand system
but after the addition of ions the protein changed its conformation and looks off.
when i continue and run energy minimization, it fails

here is the ions.mdp file i used
title = ions ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = cutoff ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions

Commands used are

  1. gmx grompp -f ions.mdp -c solv1.gro -p -o ions.tpr
  2. gmx genion -s ions.tpr -o solv_ions.gro -p -conc 0.15 -neutral -pname NA -nname CL

Thank you so much in advance

Can you provide images or a better description of what this means? Adding ions performs no physical process, so it is impossible for it to change anything about the protein’s coordinates outside of (1) rewrapping across periodic boundaries or (2) deleting residues if you tell it to by making the wrong selection for replacement.


these are the images for the .gro file before and after addition of ions

i choose the solvent when adding the atoms

there is also an error that i get that the atoms name in the topology file and gro files do not match
but i was told to ignore that because the hydrogens were added on using chimera so that is probably so error in the naming


No, your atoms are clearly out of order with respect to the topology. It’s not merely a name difference, it’s a complete mismatch of order. This is destroying your structure.

any ideas on what is going on and how i can fix it?

pdb2gmx should have produced coordinate and topology files that are in agreement. If you’re using any other version of the coordinates, or have manipulated it in some way, then you need to back up and start over from the pdb2gmx-generated, force field-compliant structure.

when i use this command
gmx pdb2gmx -f prot.pdb -q prot_clean.pdb -ignh
the pdb file doesnt have any hydrogens and the topology file does
i then added hydrogens using chimera
and then use this command
gmx editconf -f prot_cleanh.pdb -o prot_clean.gro
to generate the .gro file

Is there something i am doing wrong that might be causing this error?

Manipulating the protein coordinates after pdb2gmx is done is precisely the problem.

There is no force field that has no hydrogens; even united-atom force fields at least have polar hydrogens. Whatever is output by pdb2gmx (topology and coordinates) is correct for your chosen force field and you should not make any ad hoc changes after the fact. Whatever Chimera is adding is wrong, either in terms of compatibility with the force field’s conventions or in terms of atom order. Don’t use it.

but then i get an error that the number of coordinates in the .gro and .top files dont match

I think it’s best to back up and provide some more detail.

  1. Does pdb2gmx finish without error?
  2. Do you have some kind of ligand, and if so, how are you dealing with that?

There is a tutorial you can follow if you’re dealing with anything non-standard: Protein-Ligand Complex

The error about non-matching coordinate and topology files always means the same thing - incorrect bookkeeping of all your species. If you properly use all GROMACS utilities, you won’t get this error. If you’re doing something non-standard, then you need to be very careful about what you do, and never ignore warnings or errors that pop up.

  1. yes pdbtogmx finishes without error
  2. i have a ligand, and this is the tutorial i am following. I separate the protein and ligand and deal with them separately. and combine them together later on
    I preform the pdb2gmx step on the protein only and then the hydrogens are added to the topology file and not the pdb or gro file

I still don’t follow what this means. You should use the output of pdb2gmx and nothing else. It has everything you need for the protein.

when i use this command
gmx pdb2gmx -f prot.pdb -q prot_clean.pdb -ignh

the prot_clean.pdb file has no hydrogens added, while the file has hydrogens added. when i use them together the number of atoms is not the same as one has hydrogens and one doesnt

same goes if i use the
gmx pdb2gmx -f prot.pdb -q prot_clean.gro -ignh
the output files doesnt have hydrogen

The output of pdb2gmx -o is what you want, not pdb2gmx -q.

oh thank you so much
i cant believe something so small caused so much havoc :)