Error when trying to use grompp (missing moleculetype)

User discussions
1

GROMACS version: 2020.4
GROMACS modification: Yes/No

Hi all.

I’ve assembled an enzyme-cofactor (apo LDHA; no substrate) system in LEaP prior to gromacs. When I’ve tried to add ions using gmx grompp (gmx grompp -f ions.mdp -c 1i10-NADH_solv.gro -p 1i10-NADH.top -o ions.tpr), it throws me this error:

ERROR 1 [file 1i10-NADH.top, line 116661]:
No such moleculetype SOL

I sourced leaprc.water.opc (using OPC water with amber ff19SB force field) during creating the complex in tleap but didn’t solvate here (did this with gmx solvate). I’m assuming I just need to add the correct [ moleculetype ] somewhere but I’m not sure where this is supposed to go/where I get the information from. I used tip4p.gro during gmx solvate (gmx solvate -cp 1i10-NADH_box.gro -cs tip4p.gro -p 1i10-NADH.top -o 1i10-NADH_solv.gro) and I have a topology file for opc that I may need to either copy the contents of into my .top file or write an include statement in my .top file.

Is the solution to this issue trivial or is there more to it than what I’m thinking?

Thank you in advance
Sam

2

The solution is as simple as including the correct water topology in your system topology. That can be done either by explicitly writing the [moleculetype] entry or by adding an appropriate #include statement to an existing topology (the “normal” GROMACS approach, which is what pdb2gmx does).