[gmx-users] Protein-Ligand in bilayer
drrahulsuresh at gmail.com
Sat Aug 11 03:18:23 CEST 2018
Hi Dr. Mark.
The docked complex ( docked using auto dock ) when given as input in
charmm-gui, it ask for either mol2 file or top and prm file generated using
But then it shows some atom number mismatch and couldn’t proceed further.
The docked ligand ( pdbqt ) is converted to pdb format ( by adding
hydrogen ) using open babel.
On Sat, 11 Aug 2018 at 5:01 AM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > 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
> > better way to do such simulations?
> > --
> > *Regards,*
> > *Rahul *
> > --
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