[gmx-users] About Zn paramter

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 27 16:54:22 CEST 2010

babu gokul wrote:
> Dear all
> I am including the parameter for the Zinc in the topology file all the 
> bonded and nonbonded parameters have been included in the topology still 
> it is not accepting the parameter the Zn atom move away from the 
> coordination.

Have you actually specified bonds between the Zn and its coordinating residues? 
  Such a task is not trivial to define, and would likely require thorough 
reparameterization of all species involved.  In any case, if there are actual 
bonds, they cannot be broken.  If you are relying simply on nonbonded 
interactions to hold Zn in place, this may not work and likely represents a 
deficiency in the model.

If you can justify doing so (i.e., defend against reviewer criticism), then you 
might be able to apply distance restraints to keep the position of Zn relatively 

Always keep in mind: 


> Thanking you in advance
> E R Azhagiya singam


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list