[gmx-users] Protein ligand molecular dynamics simulation

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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