[gmx-users] Simulation of nonaqueous solvents

[David van der Spoel]

On 04/01/16 18:56, abhishek khetan wrote:
> 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:
Check our website
http://virtualchemistry.org
with validated topologies and coordinate files for about 150 liquids and 
three force fields.
>
> $ 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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se