[gmx-users] MD for two merged chains

[DimitryASuplatov]

Hello,
I have a two-chain protein. I want to merge N-terminal residue of chain
A with C-terminal of chain B. I can tweak the coordinates with pymol but
when I run energy minimization two chains split again because gromacs
fairly treats the input as a two-chain protein. 
I could switch the ATOM entries for chains A and B in the coordinate
file - so that they are in the right order - and then delete the chain
identifier, this workout will not help in more complex situations like 4
chains merge though.
Is there any option that allows gromacs not to consider chain IDs and
the order of aa in the coordinate?
Thanks. I really appreciate your help.
SDA