[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

Thank you.

I wanna know of the alternative method to carry out this simulation. other
than using charmm gui.
thank you

On Fri, Aug 10, 2018 at 2:07 PM, Abhishek Acharya <abhi117acharya at gmail.com>
wrote:

> I see. I have not used charmm-gui for building system as complex as yours,
> so I can't comment on the issue. But this is a problem specific to
> charmm-gui. I suggest you contact the authors of the web-service directly.
>
> Abhishek
>
> On Fri, Aug 10, 2018 at 10:07 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Hi.
> >
> > Thank you.
> >
> > But the system (protein ligand) is being constructed in charm gui input
> > generator, where it automatically compare the complex pdb and ligand mol2
> > file ( which will Ben uploaded ).
> >
> > On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya <
> abhi117acharya at gmail.com
> > >
> > wrote:
> >
> > > Hi,
> > >
> > >
> > >
> > > > It look so complicated to carry out a protein ligand simulation in
> > Lipid
> > > > bilayer system using charmm ff. I have a ligand with 27 atoms (
> > includes
> > > > Hydrogen ). The initial structure (monomer)  is simulated in popc
> > > > constructed using charmm gui web page. To construct the same for the
> > > > portein-ligand complex is too tedious and very problematic.
> > > > The protein-ligand complex is constructed using auto dock from the
> mol2
> > > > file download from Zinc database. The complex structure then is
> > uploaded
> > > to
> > > > charmm gui and the atom number varies with the mol2 file and pdb
> file.
> > I
> > > > find no way to change the atom order or numbering.
> > > >
> > >
> > >
> > > Why this is a problem? Whatever the numbering you get in the output,
> you
> > > can always renumber the atoms using editconf. Check gmx editconf -h.
> > > --
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> > --
> > *Regards,*
> > *Rahul *
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-- 
*Regards,*
*Rahul *