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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