[gmx-users] Protein ligand molecular dynamics simulation

lina lina.lastname at gmail.com
Mon Apr 16 18:21:30 CEST 2012

On Mon, Apr 16, 2012 at 11:01 PM, sai nitin <sainitin7 at gmail.com> wrote:
> Hi all,
> I have done complex (protein + ligand) complex from autodock software using
> this complex im trying to follow
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
> tutorial
> But when i take complex structure directly from autodock result and run
> PDB2GMX it will give error because it is not recognizing ligand topology
> which is in complex structure.
> Then i followed justin tutorial took protein alone and applied Charmm27
> Force field and used generate ligand topologies using Swissparam tool
> (http://swissparam.ch/) when i do Editconf and created cubic box ligand is
> going away from protein.
> Actually my main task to place ligand in paraticular binding site in my
> protein and perform molecular dynamics.
> Can any body tell me how to do this..?

1] pdb2gmx generate ligands.top (if possible, basically you need
generate your ligand.itp by other ways) and rename it as ligands.itp
2] pdb2gmx generate protein.top and rename it as protein.itp (also
need delete some entry)
3] create the topol.top includes the ligands.itp and protein.itp, take
care the double entry.
(To make it easy, you may take some pdb with several chains. use
pdb2gmx and see how those top files combined together.)
4] The docked structure skip the pdb2gmx step. go directly to the editconf.

You may do a try, but it will be helpful if you are a bit familiar
with how to combine those top_files.

> Thanks in advance
> --
> Sainitin D
> --
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