[gmx-users] Question: how fix protein without loops

[Ann Vakhrusheva]

Hello! 
I would like to restrain my protein but without loops before minimization. Can anyone advise me something?
I was trying to make ndx file. As I understand, in this format all residues starts from 1 and don't split into chains by numbers (I mean, for example, a chain B doesn't start from 1, but continues a chain A). My protein has 2 chains (+2 chains of DNA), so when I want to exclude loops in chain B, I get restraints starts not from beginning of chain B, but subsequent restraints starting in chain A. 
So I have the error, that my chain B doesn't correspond to the molecule and I have to move it to the right molecule (in my file 'topol_Protein_chain_B.itp' the chain B starts from 1 as separate chain). 
Maybe I can change numbering in list of residues during make_ndx? Or maybe here's another way?
Thank you for any help.