On Sat, Nov 26, 2016 at 4:32 AM, 庄灿波 <zhuangcb13.mails.jlu.edu.cn> wrote:
>
> âDear,
>
> I followed the tutorial 20 and used MCPB.py to creat the charges and
> parameters for my HEME and a ligand.
>
> And I checked the mol2 file of ligand. The charges of ligand are not
> integer.
>
> And there are some parameters (such as bond, angle) between ligand and
> FE.
>
> I want to use the parameters created by MCPB.py to calculate MMPBSA.
>
> Is the calculated MMPBSA value reasonable as the charges are not
> integer and
> some parameters between ligand and FE?
>
MM/PBSA applies *only* to non-covalently bound ligands. If there is a
chemical bond between your ligand and protein, MM/PBSA cannot be used.
HTH,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 29 2016 - 09:30:02 PST
