AMBER Archive (2005)

Subject: Re: AMBER: MM/PBSA basic questions

From: Peng Tao (amberhelp_at_gmail.com)
Date: Fri Nov 18 2005 - 12:59:39 CST

Thank you all for answering my questions. Now I got clearer idea how to do
this now.
 Best regards,
Peng Tao

 On 11/18/05, David A. Case <case_at_scripps.edu> wrote:
>
> 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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