[gmx-users] DMSO

[Hoda Alibiglou]

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