[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

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 *