[gmx-users] Question: How to delete water

[Justin Lemkul]

On 12/10/19 8:24 PM, 변진영 wrote:
> 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

Your problem is you are specifying the reference atom as 033 
(zero-three-three) instead of O33 (oh-thre-three, for Oxygen). Hence, no 
reference atoms are found and the bilayer can't be subdivided.

-Justin

> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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