AMBER Archive (2009)

Subject: [AMBER] lmod calculation for complexe

From: . .. (m.o.m_at_live.fr)
Date: Wed Feb 11 2009 - 03:09:04 CST

HI,
I want to study a ligand receptor complex (2:1), in two step, first building a complex1 with 1 ligand and 1 recpetor molecule and i start lmod calculation,
after i add a second molecule of receptor to the final structure obtained after lmod calculation= complexe2 and i start lmod calculation.
my question is ; is it correct to do:
in the first step i do retraintmask for the receptor molecule, my ligstart_list and ligend_list are the first and last atom number of ligand in complexe1 ??
in the second step do retraintmask for ""complex1"", my ligstart_list and ligend_list are the first and last atom number of complexe1 in complexe2 ??
or the igstart_list and ligend_list are the same in all calculation??
thanks
  
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