On Tue, Sep 15, 2015 at 12:50 PM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
>
> The error message was
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
>
> I went through the earlier post and changed my input files as below
>
>
> input file for running PB and GB
>
> &general
>
> endframe=5000, keep_files=2,
>
> /
>
> &gb
>
> igb=2, saltcon=0.100,
>
> /
>
> &pb
>
> istrng=0.100,inp=1,radiopt=0,
>
> /
>
>
> The programing is working .
>
>
> I have a question if one need to calculate the binding energy (ligand ,
> Protein) is these inputs are enough if not what else to be added
>
Yes, these inputs will calculate a binding free energy using the PB and GB
solvation models to estimate the solvation free energy contribution.
It omits solute entropy contributions (e.g., from normal mode or
quasi-harmonic approximations), but those are expensive and they do not
always help. You should survey the literature for a more detailed
discussion.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 15 2015 - 10:30:04 PDT
