AMBER Archive (2009)
Subject: [AMBER] hydrogen bond?
From: Jio M (jiomm_at_yahoo.com)
dear Amber users,
I have a AMBER MD run final structure which is made by residues not in AMBER itself. I want to attach some organic molecules (having donor and acceptor sites) to final structure which has hydrogen acceptor and donor sites.
is there any option in amber to make hydrogen bond for above said problem with defined angle and distance cuts? Actually I can take my structure outside amber (other softwares) to make such H bonds but there are many issues regarding detection of atoms, types, charges etc.
If I am not wrong ptraj just can help in analysing H bonds after trajectory is made.
Thanks and regards