Gromacs methanol solvate

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

I am trying to solvate a polymer chain with methanol. I have created a alcohol.rtp file in the oplsaa forcefield. The residue name is MEO and i have create methanol.gro file. I am able to solvate the polymer chain, but while using the energy minimization command [ gmx grompp -f minim.mdp -c solvate.gro -p topol.top -o minim.tpr], i am getting an error.

ERROR 1 [file alcohols.rtp, line 28]:
Invalid directive MEO

Fatal error:
Syntax error - File alcohols.rtp, line 29
Last line read:
’ [ atoms ]’
Invalid order for directive atoms

2

It appears you are trying to embed an .rtp file within a topology, which is not allowed. Only pdb2gmx reads .rtp files. A topology file follows a strict hierarchical format, as described in Chapter 5 of the manual.

3

The best approach here is : create a topology for the molecule you want and insert it as .itp file to the main topology (topol.top). @js_gro

4

Thanks for the suggestions.
I have defined methanol residue as MEO and in the .dat file i am add MEO as Others. and the polymer residues is also defined as Other.

Getting this error -Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability, and is discouraged.
is it because of less solvent molecule in the simulation box?