[gmx-users] Simulation of nonaqueous solvents

[abhishek khetan]

Is there a procedure/tutorial/method to calculate ssimulate ions in
non-aqueous solvents from scratch? By "scratch" I mean that the the
solvents I am trying to use (like dimethylsulfoxide or tetrahydrofuran or
acetonitrile) and the ions ( Li+, Na+, etc )are way simpler than the huge
protiens people usually solvate in water, but these species dont have
entries in the database that gromacs uses. I face the problem that when I
create a solvent box (dmso_box.gro, verified visually) and then try to
generate its topology file by using the command:

$ gmx_mpi pdb2gmx -f dmso_box.gro -o DMSO.gro

Where in I interactively use the forcefield as 15 (OPLS-AA) and water as 7
(none), I get the error:

Residue 'LIG' not found in residue topology database.

I am pretty sure that this must be possible by doing some other
calculations, etc to get the required data for specifying bonds, angles,
charges, their interaction parameters etc. Any help in this regard would be
highly appreciated

Best,
Abhishek