Dear all <br><br> 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 -<br><pre><i>1<span style="font-family: arial,helvetica,sans-serif;">. run genbox on initial.gro to create solvated.gro</span><br style="font-family: arial,helvetica,sans-serif;">
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 2. cp solvated.gro new_waters.gro<br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 3. use vi to remove everything in new_waters.gro except the new waters (make<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> sure you remove waters that were in initial.gro)<br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 4. use vi to edit keepbyz.pl<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> - upperz and lowerz variables as you please<br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> - sol to the name of your solvent molecule<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 5. run keepbyz.pl on new_waters.gro <br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> ./keepbyz new_waters.gro > keep_these_waters.gro<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 6. tail -1 initial.gro > last_line.gro<br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 ) initial.gro<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> <br></i><span style="font-family: arial,helvetica,sans-serif;">>></span><i style="font-family: arial,helvetica,sans-serif;"> not_last_line.gro<br>
</i><span style="font-family: arial,helvetica,sans-serif;">>></span><i style="font-family: arial,helvetica,sans-serif;"> <br></i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 8. cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro<br>
</i><span style="font-family: arial,helvetica,sans-serif;">></span><i style="font-family: arial,helvetica,sans-serif;"> 9. editconf -f new_system.gro -o new_system_sequential_numbers.gro<br><font face="arial,helvetica,sans-serif"><br>
<br></font></i></pre>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-<br>
<br>WARNING 1 [file aminoacids.dat, line 1]:<br> Bad box in file new_system.gro<br><br>I am unable to understand why it shows Bad box in file "new_system.gro" ?. Can anyone help me to solve this problem.?<br><br>
I will be really thankful for that.<br><br>Nitu sharma.<br>