[gmx-users] protein-ligand tutorial problem

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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