AMBER Archive (2000)

Subject: Organic solvents with Leap

From: Jose Ramon Blas (jramon_at_sgbq.bq.ub.es)
Date: Tue Oct 03 2000 - 19:20:58 CDT


Hi friends,

I have been trying to solvate a molecule with DMSO by using Leap. The path
followed has been this:

        i)create a residue with a unit of DMSO
        ii)create a unit containing a box of 400 Monte Carlo equilibrated DMSO
molecules.
        UNITDMSO = loadpdb dmsobox.pdb
        iii)load the solute (I call it ff1)
        iv)solvate
        solvatebox ff1 UNITDMSO 12

This creates a box with the solute properly immersed in DMSO and then I save
topology and coord files for starting MD.

After a few picoseconds of MD, several solvent molecules collapse forming
aggregates of DMSO. It's a bit strange. I must have done a wrong definition of
the solvent, but I don't know where.

Thanks in advance for your help,

                                        Blas