[gmx-users] Protein-Ligand in bilayer

[Abhishek Acharya]

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.