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>
> 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,
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users