[gmx-users] problem regarding editconf
sudheer.pbm07 at gmail.com
Sat Jan 26 11:47:29 CET 2008
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
is it right, what i have done or any chages i have to do?
pls help me.....
thanks in advance.
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