[AMBER] Pairwise Decomposition-Mask not wroking?

From: Jag Silwal <jagsilwal.gmail.com>
Date: Tue, 15 Aug 2017 12:09:21 -0400

Dear all,

I ran pairwise decomposition energy with the following script. This is a
protein-protein interaction complex AB and all I need is all the energy
associated with protein A to Protein B. But even with the mask, the system
is giving me interaction of all 273 residues to all other 273 residues
creating a massive amount of data.

May be I am missing the concept here. But could please help me understand
this here? All I need is decomposition energy associated with every
residues from receptor A to that of the ligand B. But I am getting not only
AB but also BA, AA and BB decomposition energy as well.

Could you please guide me on this?

startframe=8991, endframe=9000, interval=5,
receptor_mask=:1-212, ligand_mask=:213-273,
verbose=1, keep_files=0, strip_mask=':WAT,CL',
igb=8, saltcon=0.150,
idecomp=4, dec_verbose=1

Appreciate your help,

AMBER mailing list
Received on Tue Aug 15 2017 - 09:30:33 PDT
Custom Search