[gmx-users] toluene as a slovent

[Dallas Warren]

You also require a topology file for the toluene (.itp), include that in
the system topology file (.top):

*#include "toluene.itp"
*

Then add the molecule name and number of molecules added to the system to
the molecule section at the end of the system topology file:

[ molecules ]Toluene    254

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 2 Dec 2019 at 19:44, Iman Katouzian <imaneternity at gmail.com> wrote:

> Hello,
>
> I have downloaded the toluene pdb file and want to use it as solvent in
> GROMACS rather than the water molecules. I have added toluene as a molecule
> using gmx solvate -cs toluene.gro however, in the next steps, it is not
> added to the topol.top file and I cannot go-ahead to the next steps of
> simulation. I'd be grateful if someone can help me with this issue as I
> have not tried other solvents rather than water before.
>
> Thanks.
>
> On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian <imaneternity at gmail.com>
> wrote:
>
> > Hello,
> >
> > I have downloaded the toluene pdb file and want to use it as solvent in
> > GROMACS rather than the water molecules. I have added toluene as a
> molecule
> > using gmx solvate -cs toluene.gro however, in the next steps, it is not
> > added to the topol.top file and I cannot go-ahead to the next steps of
> > simulation. I'd be grateful if someone can help me with this issue as I
> > have not tried other solvents rather than water before.
> >
> > Thanks.
> >
> > --
> >
> > *Iman Katouzian*
> >
> > *Ph.D.** candidate of Food Process Engineering*
> >
> > *Faculty of Food Science and Technology*
> >
> > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> >
>
>
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> --
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