AMBER Archive (2005)

Subject: Re: AMBER: MM/PBSA basic questions

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 18 2005 - 11:09:05 CST

On Fri, Nov 18, 2005, Peng Tao wrote:

> 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

The general idea is this: use ptraj to strip away the solvent from your
explicit water simulation. For this you need topologies 4-6 and trajectory
files 7-9. This will create new trajectory files (say 10-12) that don't have
water.

Then, run the mm-pbsa analysis with the stripped trajectories. This will use
topologies 1-3 and trajectory files 10-12.

I'm not sure if this answers your question, but I hope so....dac

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