[AMBER] per residue decomposition MMPBSA

From: Lara rajam <lara.4884.gmail.com>
Date: Fri, 18 Sep 2015 13:03:29 -0400

Dear AMBER !

I would like to do the per residue energy decomposition for the simulation
I have done. the protein residue goes from 1-142 and the ligand goes from
143-146

I would like to know how i can do it for the residue of interest in the
protein to the whole ligand .

I used the following input

Per-residue GB and PB decomposition

&general

   endframe=50, verbose=1,

/

&gb

  igb=5, saltcon=0.100,

/

&pb

  istrng=0.100,inp=1,radiopt=0,

/

&decomp

  idecomp=1, print_res="1-142; 143-163"

  dec_verbose=1,

/



in this i have mentioned the whole protein and ligand , how i use the
residue flag to give it more specific of some cut off distance from the
ligand to the protein binding site.


thank you
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Received on Fri Sep 18 2015 - 10:30:04 PDT
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