Dear Modeller,

I want to build a model A in the presence of Model B ie to get an effect of presence of Model B on A.i used the alignment as follows

>model_A aaaaaaaaaaaaaaabbbbbbbbbbbbb >templateA aaaaaaaaaaaaaaa------------- >Model_B ---------------bbbbbbbbbbbbbb

Is this alignment correct. and what script i sould use since i want to use Model B for creating an environment but not for modelling.is this approach correct for multi chain modelling?

with regards Nadeem Ahmad