[gmx-users] GMO simulation

[RAHUL SURESH]

On Sun 14 Apr, 2019, 5:01 PM Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 4/14/19 1:51 AM, RAHUL SURESH wrote:
> > On Sun 14 Apr, 2019, 11:15 AM Ayesha Fatima, <ayeshafatima.69 at gmail.com>
> > wrote:
> >
> >> Dear All,
> >> I have a glyceryl monooleate 100 molecule assembly. I want to pull a
> >> peptide like molecule through it. I have obtained the forcefield files
> >> from *Boeckmann,
> >> Rainer website.*
> >> I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but
> >> got stuck as the force field obtained from Rainer website and put in the
> >> working directory, the path to working directory does not appear in the
> >> list of forcefields.
> >> i prepared my molecule using 54a7 forcefield implemented in ATB server.
> i
> >> got the itp files and prepared the gro file using editconf
>
> If you already have coordinates and an .itp file, then preparing the
> system is straightforward. You do not need pdb2gmx and you can prepare
> the topology by hand. I doubt that my membrane tutorial is particularly
> helpful, however this one may be more useful as it involves creating a
> topology by hand and placing a protein in an aqueous layer:
>
> http://www.mdtutorials.com/gmx/biphasic/index.html
>
> >> My question is to anyone who has done the glycerol simulation using
> >> gromacs. please help with the exact procedure to develop the simulation
> >> files. Should I add the 54a7 forcefield with to the OPLSAA updated
> >> forcefield by Prof Rainer or vice versa? I also have a peptide like
> >> molecule to pull through the GMO membrane. Any one can help guide
> through
> >> this?
> >>
> > Hi
> >
> > You must add the ff in Ur gromacs directory and not in Ur working
> > directory.
> >
> > For example, use/local/gromacs/share/gromacs/top
> >
> > And that will reflect the FF in pdb2gmx.
>
> That's not true - a modified force field can be placed in the working
> directory and pdb2gmx will actually read it first and put it in the
> selection list. Modifying force field files in the working directory is
> the preferred method in case something goes wrong; then the files in
> $GMXLIB do not get messed up.
>

Oh sorry for the wrong suggestions.

>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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