[gmx-users] Protein-Ligand in bilayer

Abhishek Acharya abhi117acharya at gmail.com
Thu Aug 9 19:53:31 CEST 2018


> 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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