[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

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 *