On Fri, Sep 18, 2015 at 1:03 PM, Lara rajam <lara.4884.gmail.com> wrote:
> 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.
>
You can't. MMPBSA.py prints out pairwise interactions between all pairs
of residues in the print_res selection. There is no way to modify this
behavior.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 11:00:05 PDT
