[gmx-users] Topology file

[Mahdi Sobati Nezhad]

Thanks rose for your help.
so for ligand and protein interaction its better that I use position
restraints


On Wed, 10 Oct 2018 17:07 rose rahmani, <rose.rhmn93 at gmail.com> wrote:

> First, i think it's better to ask WHY
> http://www.gromacs.org/Documentation/How-tos/Position_Restraints
> That's why people use position restraints.
>
> About WHEN, <for example> sometimes your molecule behavior is different in
> box. For instance you study the interaction of your molecule with surface.
> So the molecule need to be free and move in a box to find its best
> configuration toward surface. Because its properties may differ in
> different part of box. You can't put a restriction on it, because it's
> distance and configuration, is crucial in interacting with surface...
> Maybe it's not a scientific explanation of an issue( as justin masterly do)
> but i just tried to share my experience. Hope it helps!
>
> Best
>
> Rose
>
>
>
> On Wed, 10 Oct 2018, 16:21 Mahdi Sobati Nezhad, <
> mahdisobatinezhad at gmail.com>
> wrote:
>
> > Thanks rose. Can you tell me more about which cases I should use position
> > restrictions?!
> > Thanks
> >
> > On Fri, 5 Oct 2018 10:33 rose rahmani, <rose.rhmn93 at gmail.com> wrote:
> >
> > > Hi,
> > >
> > > It depends on you, wheter you want to put position restriction on your
> > > molecule you should add posre.itp to topol.top or not.
> > > But whenever you use define=-DPOSRES in your .mdp file, GROMACS can
> read
> > > posre.itp files in topol.top an apply position restriction to molecule.
> > >
> > > Rose
> > >
> > > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, <
> > > mahdisobatinezhad at gmail.com>
> > > wrote:
> > >
> > > > Hello Gromacs users.
> > > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top
> there
> > > is
> > > > no any porse.itp
> > > > What can I do?!
> > > > Do it's important that porse.itp should be in topol.top or its enough
> > > that
> > > > pdb2gmx make porse.itp?!
> > > >
> > > > Thanks
> > > > --
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