Dear Amber users,
I have a little question about MMPBSA
calculation between my protein and DNA. I'm performing a binding
calculation with residue decomposition using this input file:
&general
verbose=2, netcdf=1,
/
&gb
igb=5, saltcon=0.100,
/
&decomp
idecomp=2,
dec_verbose=1, csv_format=0,
/
I omit the print_res flag
since I want to check which are the residues that contribute to the
binding. I get some positive records for some specific Arg resides that
interact with the DNA, but also obtain the same energy values for some
Arg residues that are clearly far away from the binding region and
therefore, shouldn't be contributing to the binding of the complex.
Is
it MMPBSA calculating not only the binding of the complex but also
inside the complex and the receptor? Has it any sense?
Best regards,
Fernando
--
==============================================
Fernando Martín García
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/
==============================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 14 2013 - 06:00:01 PST
