Alchemical process (pmx)

User discussions
1

GROMACS version:2023.3
GROMACS modification: No
I am looking for some help on following pmx tutorial.
[Protein mutation — pmx documentation](https://pmx tutorial site)
(i do not have older python so I used web_pmx) While
gmx grompp -f genion.mdp -c water.pdb -p newtop.top -o genion.tpr -maxwarn 2
where I ignore the mismatch. The warning look like this.
"atom name 13 in newtop.top and water.pdb does not match (HD21 - 1HD2)
atom name 13 in newtop.top and water.pdb does not match (HD21 - 1HD2) etc
"
I believe it run minimization successfully. However, at equilibration with position restraints, I have some trouble.
I copied enmin.gro to restraint.gro and run
‘gmx grompp -f f_npt.mdp -c enmin.gro -p …/…/newtop.top -o npt.tpr -maxwarn 1’

I got WARNING 1 about barostat,
"WARNING 2 [file hybrid_posre.itp, line 48]:
Some parameters for bonded interaction involving perturbed atoms are
specified explicitly in state A, but not B - copying A to B
"
"WARNING 3 [file newtop.top, line 15]:
The bond in molecule-type Protein_chain_A between atoms 117 DCD1 and 121
DCE1 has an estimated oscillational period of 7.1e-03 ps, which is less
than 5 times the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.

Analysing residue names:
There are: 20 Protein residues
There are: 1863 Water residues
There are: 11 Ion residues
"
Should I ignore warning #2? Thank you very much.

2

Hi, It might be beneficial to ask your question on the PMX Forum as your question appears to be more related to PMX tutorial rather than GROMACS. They should be able to provide you with more specialized assistance.

3

Yes, this question was not appropriate here. Thank you very much.