[gmx-users] preparing pdb file

[elham tazikeh]

Dear Gmx users
i have problem with making pdb(s) of proteins that have 2 chain or more.
my question is:

if in a protein, the active site for two of them (chains) are the same and
there is not any advantages one site to another site in chains...which one
is choiced?chain A or B?

for example: in pdb:2BXG (HSA+IBUPROPHEN); there are 2 chain and 3
sub-domains.
there are Ibuprophen (AC1 , AC2) molecules in domains 3,4,5.
i dont know which one of chains (A or B) is appropriate for study?
thanks a lot for any tip