[gmx-users] zn finger simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 20 12:51:02 CEST 2011

> Dear all
> I am trying to run a simulation of a dimer including a zinc finger using 
> Gromacs 4.5.3. I have gone through the documentation and searched the 
> forums but could not find a specific answer to my problem.
> In order to produce the initial topology (top) and coordinate (gro) 
> files for the simulation I am running pdb2gmx using the PDB structure of 
> the complex, including the Zn ions. I realized that for them to be 
> constrained in their position, i.e. in the Zn finger, I should create 
> bonds editing the specbond.dat file. I introduced the following lines:
> CYS     SG      1       ZN      Zn      1       0.23    CYS     ZN
> HISE    NE2     1       ZN      Zn      1       0.21    HISE    ZN
> and updated the counter from 8 to 10. Needless to say, the Zn atoms are 
> coordinated to His and Cys residues in the first protein. The distances 
> correspond to what I measured using VMD. However pdb2gmx did not seem to 
> be linking the aforementioned residues. I then moved the Zn lines in the 
> PDB to the end of the section in the PDB file corresponding to chain A, 
> the one with the Zn fingers. Then the links were produced. So the first 
> question is: should one move the special atoms to the chain to which 
> they supposedly correspond?

Yes.  Chain identifiers must be continuous, per the way pdb2gmx now works.

> After successfully pdb2gmx-ing, I tried the Gromacs preprocessor 
> (grompp). It complained producing 138 errors like. 
> ERROR 132 [file PDBcode_forcefield_Protein_chain_A.itp, line 13663]:
>   No default Proper Dih. types /   No default Angle types
> By looking at the lines in the itp file for the chain A I found that the 
> errors referred to the lack of dihedrals or angles of the Zn atoms with 
> their partners. Could you give some suggestions on how to produce these 
> missing parameters?

This is no trivial task.  Instead of using formal bonds via specbond.dat, why 
not try using simple distance restraints, which can be added to the topology 
after pdb2gmx?  See manual section 4.3.4.



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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