[gmx-users] Protein-Ligand in bilayer

Mark Abraham mark.j.abraham at gmail.com
Sat Aug 11 01:31:00 CEST 2018


Does CHARMM-GUI not provide a output coordinate file that matches the
generated topology file? I don't know why you find its change of ordering a


On Thu, Aug 9, 2018, 18:48 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> 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 *
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