Add ions and show system haas non-zero total charge

User discussions
1

I have a peptide that has been designed and edited from cardiac troponin (PDB: 4Y99). I want to simulate graphene sheets with the peptide, but before that, I want to do a simulation on the peptide like the Lysosim Water tutorial on Gromacs.
I’m using charmm36-jul2022.ff and having some trouble when add some ions

Command that I used from make topology until add ions:
Build Topology : gmx pdb2gmx -f protein_edit.pdb -o protein-process.gro -missing - for this task is succeed
[I using -missing because that is protein edited so many amino acid missing]

Define Box : gmx editconf -f protein_process.gro -o protein_newbox.gro -c -d 1.0 -bt cubic - for this task is succeed

Solvate : gmx solvate -cp protein_newbox.gro -cs spc216.gro -o solv.gro -p topol.top - for this task is succeed

Add ions : gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I using parameter couloumbtype PME as the example below:
[file ions.mdp]
; ions.mdp - used as input into grompp to generate ions.tpr
; 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 < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization 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 ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

And I get some trouble like this :
NOTE 2 [file topol.top, line 5761]:
System has non-zero total charge: -0.260000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 5761]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.

But when i change the parameter coloumbtype cuttoff in ions.mdp it show like this
NOTE 2 [file topol.top, line 5761]:
System has non-zero total charge: -0.260000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

Analysing residue names:
There are: 35 Protein residues
There are: 13393 Water residues
Analysing Protein…
Number of degrees of freedom in T-Coupling group rest is 82173.00

NOTE 3 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.

So How to solve the problem?

2

It seems like there are some atoms missing, lead to the non-integer charge.
When I find the amino acids missing, I prefer to use some modelling tools like SWISS-MODEL or AlphaFold to fix then, rather than using the dangerous option “-missing”. Even more, if the missing amino acids are far from the domain which I am interested in and do not significantly contribute to the secondary structure, I think it is also reasonable to compeletely delete the incomplete amino acids .

1 Like
3

Thanks for the explanation. and I already do what you said, and it works. Thanks a lot