[AMBER] hydrogen bond?

From: Jio M <jiomm.yahoo.com>
Date: Sun, 9 Aug 2009 12:29:23 +0100

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.

please suggest.

Thanks and regards

Jio

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 21:09:22 PDT
Custom Search