[gmx-users] Protein ligand molecular dynamics simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 16 17:03:50 CEST 2012

sai nitin 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..?

Whatever you're doing is changing the coordinates that you originally had.  You 
don't want to do that.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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