GROMACS version: 2020.4
GROMACS modification: No
Here post your question
I think that it should be a trivial question for most of you, but I do have a protein that I would like to run into a water/ions box. The protein (pdb files) already contains some water molecules (crystallographic ones).
I am following Justin’s tutorial with amber99sb.ff
If I use tip3p / spc216.gro model, everything goes well up to the minimization step.
However, if I try to use tip4p / tip4p.gro, the pdb2gmx step crashes with errors concerning the ghost atom on these water molecules : WARNING: atom MW is missing in residue HO4 XXX in the pdb file.
Hi,
I guess that residue HO4 is one of the crystallographic water. Or? You can remove the crystallographic waters before running pdb2gmx or you can add the missing particles to the crystallographic water.
The warning comes since TIP4P water is a 4-particle model, while TIP3P /SPC are a 3-particles model .
Best regards
Alessandra
Yes indeed, the bugging residues are the crystallographic waters.
However, while I do understand the difference between tip3p and tip4p (3 points and 4 points models), I don’t understand why for tip3p pdb2gmx generates the water molecules by adding the H atoms from the only O atoms defined in the PDB, while it is not able to do it for tip4p…
Best regards
Xavier
my guess is that pdb2gmx in the case tip4p needs to add not only H (defined in the force field hydrogen bond database hdb), but also an extra particles MX (that is not a hydrogen) and it does not have information where to locate MX. You can have a look at the force field fields and probably fix it.
This is exactly what I think, a kind of issue in the amber14sb FF. But on another machine with GMX 2019.4 installed the waters are correctly processed. I will have to find where to look for this issue.
Meanwhile, I’ve installed GMX 2021, same issue.
In order not to loose to much time, I’ve launched my MDs with TIP5P waters…