AMBER Archive (2005)

Subject: Re: AMBER: MM/PBSA basic questions

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Fri Nov 18 2005 - 11:06:04 CST

Hi,

MM_PBSA is a postscript. You are right. You need use trjectories of MD with
explicit water to run MM_PBSA. When you generate .crd files for snapshots, you
don't need any topology files because you need to indicate only resid you want
to output. But when you calculate free energy, you need topology files for
proteins without water and counterions.

Usually, people have two ways to do MM_PBSA. One is to use only a single
trajectory of a complex. The other is to use trajectories for both a complex
and unbound molecules. You can see that the first way costs less time. Free
energy is not converged during nanoseconds. It turns out that the first way can
get better results if no significant conformational change because some errors
are canceled.

Hope this helps!

Wei Chen

Quoting Peng Tao <amberhelp_at_gmail.com>:

> Dear All,
> I am trying to use MM/PBSA to analyze my MD results of a complex of Protein
> and peptide. Before start to use MM/PBSA from AMBER8, I really want to make
> several things clear to myself. I have read MM_PBSA manual and Examples come
> from AMBER8, and several emails on this mailing list about MM/PBSA. But
> still, I am not sure about the several questions.
> Here are list of what I have right now.
> 1. topology file of protein alone
> 2. topology file of peptide alone
> 3. topology file of complex of protein and peptide
> 4. topology file of protein and TIP3P Water
> 5. topology file of peptide and TIP3P Water
> 6. topology file of complex of protein and peptide and TIP3P water
> 7. trajectory file of protein with TIP3P water
> 8. trajectory file of peptide with TIP3P water
> 9. trajectory file of protein and peptide complex with TIP3P water
> Please notice that the number of TIP3P water with protein or peptide or
> complex are different, because I added them by LEaP separately.
> It seems to me that I can use trajectory of MD with my system in explicit
> TIP3P water to run MM/PBSA. But I am not 100% sure.
> Here I want ask the following questions.
> 1) Can I use trajectory of MD with my system in explicit TIP3P water to run
> MM/PBSA?
> 2) If the answer is YES for question 1, then which topology file I need to
> use to generate snapshot from my MD trajectory? I mean, the topology file to
> run SANDER is the one with explicit TIP3P water. But MM/PBSA doesn't need
> explicit water information. Should I use the topology file of Protein alone
> (without explicit TIP3P water) to generate snapshot from trajectory file for
> protein with explicit TIP3P water? Will this confuse MM/PBSA (topology file
> WITHOUT water combines with trajectory file WITH water)
> 3) If I want to calculate binding energy of protein and peptide, can I use
> snapshots from the different trajectory? I mean, I generate snapshots from
> trajectory file of protein with TIP3P water for protein, snapshots from
> trajectory file of peptide with TIP3P water for peptide, and snapshots for
> complex from trajectory file of protein and peptide complex with TIP3P
> water. Then use these snapshots to calculate binding energy.
> Thank you all for your answers.
> Best regards,
> Peng Tao
> 

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