[gmx-users] protein-ligand tutorial problem

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 11 23:16:35 CET 2012

rama david wrote:
> Hello
>                 I am doing JUSTIN Protein-ligand tutorial.
> I complete your Lysozyme tutorial before these one.
> I complete tutorial upto the make-ndx
> but after giving command grompp for nvt.tpr
> production..
>  I get the following error
> No molecule were defined in the system ,
> I know somewhere I make mistake while following
> instruction , but  I did it for 3 times,so
> please help me to check my mistake
> (i am using GROMACS 4.5.4 )
> After giving the command make_ndx
> I choose the option system..Is
>  it the error source???

Potentially.  The tutorial never has you use the "System" group for anything. 
Follow instructions closely.

The original error suggests that you have either not defined any molecules in 
the [molecules] directive of the .top (unlikely), there is otherwise some 
mismatch between the two, or the index file is incorrect.  The last two are the 
most likely possibilities.



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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