[gmx-users] heteroatom not to be a ligand

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 3 22:11:20 CEST 2011

ahmet yıldırım wrote:
> Dear users,
> I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is 
> heteroatom, it is not a ligand.
> I think I shouldn't use a way as Justin tutorial 5. Because X is not a 
> ligand. what should I do?

If it's not relevant to the dynamics (as is often the case with unnatural 
compounds in crystal structures), you can probably delete it.  The structure may 
require extensive equilibration to combat any artifacts of its removal.



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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