[gmx-users] problem regarding editconf

sudheer babu sudheer.pbm07 at gmail.com
Sat Jan 26 11:47:29 CET 2008

hi all,
i have one problem regarding 'editconf' for using add simulation box, my
protein contain 59 residues + crystal water -103 molecules
In one tutorial they have used following command for add simualation box
1.editconf  ­bt cubic –f fws.pdb –o fws.pdb –d 0.9    - in this 0.9 is nm

 i have reffered in gmxusers(archives) they have used following command for
adding simulation box and water
 1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9.0000 -c
 2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top

based on above things i have used following commands for adding simulation
box and water

1.editconf  ­bt cubic –f fws.pdb –o fws.pdb –d 0.4    - in this 0.4 is nm
2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  prot.top
program was finished without error and it added 4884 water molecules around
my protein
is it right, what i have done  or any  chages i have to  do?

pls help me.....
thanks in advance.
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