[gmx-users] Ligand-ligand Tutorial

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 14 18:15:02 CET 2012

Hovakim Grabski wrote:
> Hi,
> Anyone know any ligand- ligand tutorial?

If there is no receptor, then there is no ligand ;)

> I've been trying to set up a taurine  simulation with 
> lysophosphatidylcholines (LPC) with no success.

Without a description of what you've tried, what hasn't worked, etc then there's 
not much anyone can suggest.  If you've simply got two small molecules you want 
to simulate together:

1. Obtain topologies for both species and construct a .top that calls a force 
field and the small molecule topologies
2. Set up the coordinate file such that the two species are arranged how you'd 
like them in a single box (done with editconf)
3. Solvate and proceed as you would any other simulated system



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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