[gmx-users] Help regarding terinary complex simulation with ZN at active site

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 28 19:28:53 CET 2011

kala wrote:
> Dear friends
>                 I am trying to run a MD simulation with a Zn ion in the 
> active site. The zinc makes covalent bond to His , Asp , Cys and Drug 
> molecule. however I am trying to study various ligands that make a 
> sustainable bond with zn over period of time. I am new to gmx and I am 
> pretty confused with .rtp and specbond.dat . How should I make His (its 
> actually HisD) , Asp and Cys bonded with Zn and enough residual charge 
> on zn with which it can form a bond to ligand molecule. will definitions 

Bonds do not break or form during MD, unless you are doing QM/MM.

> of bond lengths and bond angles on specbond.dat will alone suffice ? I 
> am using Amber99sb ff so that I can carry out md on my fermi card. any 
> help is highly appreciated.

You can define bonds in specbond.dat between your protein residues and the Zn 
ion, but there are no bonded parameters for such interactions in that force 
field, by default.  Thus you will either have to parameterize them yourself or 
define some arbitrary distance restraints (thus not using specbond.dat).

You also face the challenge that in such a species there will likely be 
significant inductive effects requiring a re-parameterization of the active 
site.  What's more, a static representation of these charges may not be 
sufficiently accurate.  There are various QM/MM papers that have shown this.

Take note of the points raised in the "Exotic species" entry here:



> thanks and regards
> bharath


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