[gmx-users] DMSO

Hoda Alibiglou hoda.alibiglou at gmail.com
Tue Dec 20 17:08:22 CET 2016


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

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,


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