Organic solvents with Leap

From: Jose Ramon Blas <>
Date: Tue 3 Oct 2000 17:20:58 -0700

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
        UNITDMSO = loadpdb dmsobox.pdb
        iii)load the solute (I call it ff1)
        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,

Received on Tue Oct 03 2000 - 17:20:58 PDT
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