[gmx-users] Ligand-ligand Tutorial

[Justin A. Lemkul]

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

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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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