[gmx-users] problem regarding editconf

[sudheer babu]

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080126/83cfc734/attachment.html>