Re: [AMBER] Very low MMPBSA result

From: Nada Afiva <>
Date: Thu, 16 Apr 2020 02:36:01 +0700

Dear Prof. Case,
Thanks so much for your suggestions.
Now it is solved.
The problem is the promtop file.
For mmpbsa calculation. it is good to use the prmtop file extracted from MD
Thank you so much.

Best regards,

Pada tanggal Sel, 14 Apr 2020 pukul 19.26 David A Case <> menulis:

> On Tue, Apr 14, 2020, Nada Afiva wrote:
> >
> >2. Look at all three structure visually to make sure they are what you
> >want.
> >Ans: Really, I don't have any idea how to visualize prmtop files.
> >Yesterday, I make pdb file using cpptraj command with input prmtop and rst
> >file for certain time of simulation, and it can be visualized well.
> Looking at the pdb file coming from prmtop + coordinates is what I
> meant.
> >
> >
> >4. and try to figure out why the sum of the ligand + receptor bond energy
> >is not the same as the complex bond
> >energy.
> >Ans: Here really I do not have idea also.
> Look at the mdout file for each of the three minimizations. Get the
> bond energy, and check to see if receptor + ligand = complex. In the
> single trajectory approach, the ligand coordinates (for example) will be
> the same in the "ligand" coordinate file as in the "complex" coordinate
> file. So the ligand contribution to the bond energy will be the same.
> Same idea for the receptor.
> If the bonded energy differences are all zero, look for any large
> differences in other components of the energy.
> ....dac
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Received on Wed Apr 15 2020 - 13:00:02 PDT
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