[gmx-users] Equilibrate the water around my molecule

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 26 21:05:50 CEST 2012

Lara Bunte wrote:
> Hi
> with the -ter option I got the same errors. I read in the manual something about the termini database but I don't understand what that s about (I didn't study Chemistry...). 

Well what choices did you make regarding termini?  Telling us you invoked the 
option doesn't help us diagnose what is wrong (either with the program, the 
input files, or whatever you did).

> I read this tutorial page but that doesn't help me :-(
> Could you explain me in your words what it has to do with this termini? Thanks

If you tell pdb2gmx that your residue is a protein, it will treat it as a 
protein.  Therefore, pdb2gmx is going to treat its termini as if they were amino 
acids, building the appropriate N- and C-terminal atoms.  If you're not familiar 
with what this means, open up any basic biochemistry textbook and spend a few 
moments studying what the structures are.

Your isoalloxazine structure is not composed of amino acids and thus does not 
have N- and C-termini.  Choosing "None" for your termini will tell pdb2gmx to 
not modify any of the constituent atoms.  I do not know if you have tried this 
or not.

I wonder why you are starting over with pdb2gmx?  You've posted a number of 
times regarding an .mdp file problem, which suggests you already have a suitable 
topology.  Thus there is no need to go back to pdb2gmx and try to regenerate it. 
  There is nothing magic or different about calling your residue "Protein" at 
this stage if all there exists is a simple naming mismatch in an .mdp file. 
Perhaps I've missed something along the way.



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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