[gmx-users] Protein-Ligand in bilayer

[Abhishek Acharya]

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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