[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

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 *