[gmx-users] DMSO

[tasneem kausar]

Check the total number of atoms in DMSO molecule.
after grompp you got an error of non-matching atom in gro and top file.
Subtract the number of molecule of top  file from molecule of gro file.
Divide the subtracted number with coordinates of DMSO. This gives the
number of DMSO molecule. Add this number to the top file.

Hope this will help

On Tue, Dec 20, 2016 at 9:38 PM, Hoda Alibiglou <hoda.alibiglou at gmail.com>
wrote:

> 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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