Dear Amber users,
I'm trying to calculate the binding energy of a
system composed by a protein (homodimeric) and a 20-mer DNA using
MMPBSA.py. After reading this topic in the Amber mail list:
http://archive.ambermd.org/201012/0545.html
I have deduced that
entropy calculation can be introduced using three methods: a
quasi-harmonic method (entropy=1), using normal modes for receptor and
ligand or using two alternatives dynamics, one of the ligand and other
of the receptor, separately in order to introduce this entropy energy
element. This is where I have some doubts: these two dynamics are
completely independent of the original complex dynamic or are extracted
with some option (ambermask?) during the simulation?
On the other
hand, could I have some problems if I define a complete DNA (20-mer) as
ligand and this homodimeric protein as receptor, considering I have some
"gaps" in the sequence?. I have some energy errors (my mutant binds
strongly than my wild-type protein) and I don't know if I have some
mistake .
Thank you,
Best regards,
Fernando
--
==============================================
Fernando Martín
García, PhD.
Molecular Modeling Group - Lab 312.1
Molecular Biology
Center "Severo Ochoa"
C/ Nicolás Cabrera, 1.
UAM University.
Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34)
91-196-4420
Web:
http://fertoledo.wordpress.com/
==============================================
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Received on Fri Feb 21 2014 - 08:00:02 PST
