[gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer

[Justin A. Lemkul]

nitu sharma wrote:
> Dear all
> 
>                      I am running keepbyz.pl script to remove unwanted 
> waters from hydrophobic core of lipid . I am getting problem in this 
> process. For this I follow the chris neale rule -
> 
> /1. run genbox on initial.gro to create solvated.gro
> 
> />/ 2. cp solvated.gro new_waters.gro
> />/ 3. use vi to remove everything in new_waters.gro except the new waters (make
> 
> />/ sure you remove waters that were in initial.gro)
> />/ 4. use vi to edit keepbyz.pl
> 
> />/    - upperz and lowerz variables as you please
> />/    - sol to the name of your solvent molecule
> 
> />/ 5. run keepbyz.pl on new_waters.gro 
> />/    ./keepbyz new_waters.gro > keep_these_waters.gro
> 
> />/ 6. tail -1 initial.gro > last_line.gro
> />/ 7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 ) initial.gro
> 
> />/   
> />>/ not_last_line.gro
> 
> />>/     
> />/ 8. cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
> 
> />/ 9. editconf -f new_system.gro -o new_system_sequential_numbers.gro
> 
> 
> 
> /
> 
> I have successfully completed all the step but getting problem in 
> completing last step i.e editconf step  , in the last file 
> new_sequential_numbers.gro which is made by editconf unable to keep 
> solvent molecules which is present in "new_system.gro ". Also one 
> warning came during the last editconf process i.e-
> 
> WARNING 1 [file aminoacids.dat, line 1]:
>   Bad box in file new_system.gro
> 
> I am unable to understand why it shows Bad box in file "new_system.gro" 
> ?. Can anyone help me to solve this problem.?
> 

What does your "new_system.gro" have on the last line?  Have you specified the 
correct number of atoms on the second line of the .gro file so that editconf is 
reading the correct line to determine box vectors?

-Justin

> I will be really thankful for that.
> 
> Nitu sharma.
> 
> 
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> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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