hi all,<br>
i have one problem regarding 'editconf' for using add simulation box,
my protein contain 59 residues + crystal water -103 molecules<br>
In one tutorial they have used following command for add simualation box<br>
1.editconf bt cubic –f fws.pdb –o fws.pdb –d 0.9 - in this 0.9 is nm<br>
<br>
i have reffered in gmxusers(archives) they have used following command for adding simulation box and water<br>
1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9.0000 -c<br>
2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top<br>
<br>
based on above things i have used following commands for adding simulation box and water<br>
<br>
1.editconf bt cubic –f fws.pdb –o fws.pdb –d 0.4 - in this 0.4 is nm<br>
2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p prot.top <br>
program was finished without error and it added 4884 water molecules around my protein<br>
is it right, what i have done or any chages i have to do? <br>
<br>
pls help me.....<br>
thanks in advance.