Constant ph Molecular dynamics using phbuilder

User discussions
1

I am trying to perform constant ph molecular dynamics using gromacs.
I install phbuilder. I also install gromacs gromacs-2024.4 and gromacs_3.3.3_cphmd_v1.3.

But when I neutralize the system It get error message.
phbuilder neutralize -f box.pdb -conc 0.10 -solname TIP3
phbuilder :
phbuilder : WARNING - The GROMACS constant-pH beta does not appear to be loaded. While this might be fine for
phbuilder : gentopol and genparams, it MUST be loaded when using neutralize. Please source or module
phbuilder : load the GROMACS constant-pH beta.
phbuilder :
phbuilder : Running neutralize…
phbuilder : No previous ions detected in box.pdb.
phbuilder : Getting the net-charge of the system (running grompp, this can take some time for larger
phbuilder : systems)…
phbuilder :
phbuilder : ERROR - Failed to run “grompp -f ions.mdp -c box.pdb -p topol.top -n ions.ndx -o ions.tpr
phbuilder : -maxwarn 0” (exitcode 1). Check your logfile (ions.log)
phbuilder :

Thanking you in advance

2

It looks like you did not source the GMXRC for the build of the GROMACS constant-pH version.

3

Thank You sir for reply. Now I do the constant ph MD as in the following tutorial.

But in the gmx genion steps I get the following error.
gmx genion -s genion.tpr -o solvions.gro -p topol.top -pname SOD -nname CLA -conc 0.15 -neutral -cphcoupled -rminprotld 2.0 -rminld 3.0 -rtolld 0.3 -nobackup

The error is:

For the solvent search, min. dist to non-solvent: 2.00, distance to residue 2.70 - 3.30 (tolerance included)
877600 of 877739
Found 867438 suitable solvents
Lambda dyn counterion: Determining solvent molecules suitable for each residue…

The following protonable residues have 0 suitable water for counterion/buffer placement: 2 19 31 32 38 39 58

Program: gmx genion, version 2024-dev-20241209-eba91f0-unknown
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 321)

Fatal error:
Some residue have no suitable solvent for buffer/counterion placement. Maybe
try a bigger box?

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Although I set the box size 30 nm as in the following command.
gmx editconf -f prot.gro -o box.gro -box 30 30 30 -c -bt cubic