[gmx-users] Question: How to delete water

[변진영]

Dear All,
I have gone through the Justin Lemku tutorial for KALP_15 in DPPC. I have reach the last command line in step3 and faced one problem.
When I tried  to delete water in my system by running the command line:
 
 Perl water_deletor.pl -in system_solv.gro -out system_solv.fix.gro -ref 033 -middle C50 -nwater 3

The result message says that 

 Starting water deletion process… 
 Option -nwater not set, assuming 3 atoms in the water model. 
 Defining the middle of the bilayer as z = 3.27570634920635.
 ntop = 0
 Illegal division by zero at water_deletor.pl line 219.

The tutorial said that the -nwater flag defines how many atoms constitute a water molecule and for SPC, there are 3 atoms and so I used the -nwater option in my command line. 
But the message says “Option -nwater not set, assuming 3 atom in the water model.” How can I set the -nwater option? 
Any idea on what caused this problem?

-Jinyoung