Dear Canbo,
> On Nov 26, 2016, at 3:32 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.
>
Do you mean the total charge of the ligand is not an integer after RESP fitting?
> 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?
>
Can you specify which kind of property you want to calculate though MMPBSA (e.g. binding free energy of ? )?
>
> The other question is about the tutorial 20 about creating HEME parameters.
> [1]URL:http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
>
> In this tutorial the total charges of HEM.mol2 file are zero, however, the
> charges of protoporphyrin are -4. In my protein, I set the charges of
> protoporphyrin. Is it correct?
>
>
The charge of protoporphyrin should be -4. Thanks for you noticing that. I will modify the tutorial webpage later.
Kind regards,
Pengfei
> I am looking forward your replay.
>
>
> Thank you,
>
> Canbo Zhuang
>
> References
>
> 1. http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
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Received on Mon Nov 28 2016 - 13:30:03 PST
