AMBER Archive (2005)

Subject: AMBER: MM/PBSA basic questions

From: Peng Tao (amberhelp_at_gmail.com)
Date: Fri Nov 18 2005 - 09:41:26 CST

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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