[gmx-users] Spacing

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 17 14:38:06 CEST 2009

P.R.Anand Narayanan wrote:
> Dear gromacs users,
> I've been using gromacs to run a simulation of  a protein with a 
> cofactor and a ligand. i had a problem while running the simulation; the 
> cofactor, ligand and the substrate molecule were spaced away from the 
> protein in the solvent box., thereby creating literally zero interaction 
> energy.
> How do I solve this problem and place all the molecules together in the 
> solvent box?

You have several options:

1. Obtain crystallographic coordinates of the proper complex.
2. Use docking software to place the ligand in the active site.
3. Careful use of editconf on each component of the system to place them 


> Thanking you,.
> Anand.
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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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