[gmx-users] DMSO

Mark Abraham mark.j.abraham at gmail.com
Wed Dec 21 11:37:28 CET 2016


First, have you got your system working with just protein and water? And
just Protein, water and DMSO?


On Wed, Dec 21, 2016 at 3:08 AM Hoda Alibiglou <hoda.alibiglou at gmail.com>

> Hello
> I am simulating a protein in mixture of water and DMSO, I madE the box
> including water and DMSO and my protein, now I should add ions by this
> command,
> gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr
> but, each time I get an error because the number of atoms in my
> topology file and
> dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
> DMSO molecules number manually, now my error is that DMSO is unknown,
> also I used some references and according them I choosed gromos96
> forcefield for DMSO-WATER MIXTURE.
> may I ask you please to help me ?
> Best regards,
> Hoda
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