[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

Hi Dr. Mark

I have already posted in the respective forum. I am just looking for some
alternative method or to know if I am doing it wrong.!

But anyway I overcame this error.

After docking, add respective hydrogens and save it as mol2 file. Make it
as complex with protein and save as PDB. These two files can be added as
input to charmm-gui.

I have used autodock for docking and Discovery studio for conversion.

Thank you



On Sat, 11 Aug 2018 at 10:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> None of those are GROMACS tools, so you will probably do better asking
> elsewhere. But why not generate the topology after the ligands atoms get
> sorted?
>
> Mark
>
> On Sat, Aug 11, 2018, 04:18 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
>
> > Hi Dr. Mark.
> >
> > The docked complex ( docked using auto dock ) when given as input in
> > charmm-gui, it ask for either mol2 file or top and prm file generated
> using
> > paramchem.
> >
> > But then it shows some atom number mismatch and couldn’t proceed further.
> >
> > The docked ligand ( pdbqt ) is converted  to pdb format ( by adding
> > hydrogen ) using open babel.
> >
> > Thank you
> >
> > On Sat, 11 Aug 2018 at 5:01 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Does CHARMM-GUI not provide a output coordinate file that matches the
> > > generated topology file? I don't know why you find its change of
> > ordering a
> > > problem.
> > >
> > > Mark
> > >
> > > On Thu, Aug 9, 2018, 18:48 RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
> > >
> > > > Hi users.
> > > >
> > > > 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.
> > > >
> > > > I feel I m taking a wrong way in these type of simulations. What can
> be
> > > the
> > > > better way to do such simulations?
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul *
> > > > --
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> > --
> > *Regards,*
> > *Rahul *
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