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

nitu sharma sharmanitu35 at gmail.com
Fri May 22 07:18:27 CEST 2009

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

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.?

I will be really thankful for that.

Nitu sharma.
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