Sorry if my previous e-mail was misunderstood. Decomposition analysis can be
achieved with Amber 10, just not using MMPBSA.py. You can run decomposition
analysis using sander and/or mm_pbsa.pl with Amber 10.
-Bill
On Wed, Mar 23, 2011 at 10:38 AM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear Ray,
> My understanding is that decomposition analysis needs Amber 11 not Amber
> 10
> ...is there a role in AmberTool in that? sorry correct me if I
> understand
> wrong?
> Thanks
> Mahmoud
> On 3/23/11 4:24 PM, Ray Luo, Ph.D. wrote:
>
> Dear Mahmoud,
> Is there any reason that you cannot install the latest free AmberTool
> release? Also, are you using the mmpbsa perl script for this? Can you
> run
> the example?
> All the best,
> Ray
>
> On Wed, Mar 23, 2011 at 7:20 AM, Mahmoud Soliman <[1]
> mahmoudelkot.gmail.com>
> wrote:
>
> Dear All,
> In our group we only have Amber 10 installed on the cluster and as I
> know
> decomposition analysis PBSA calculation can not be done using Amber
> 10.
> Let
> me quickly explain to you the piece of work I am trying to
> investigate
> using
> Amber. I would like to explore the influence of the nearby active
> site
> residues on the ligand binding to the enzyme. Mutation of some of
> these
> residues resulted in a complete loss of the enzyme activity. I was
> planning
> to run PBSA calculation to see how each residue contributes to the
> overall
> binding using the decomposition analysis method but I realized that
> Amber10
> can not achieve this.My question is can I calculate the total binding
> energy
> for the wild type then do the same thing for a particular mutant, I
> wonder,
> can that give me an estimate on the contribution of this residue that
> I
> have
> mutated to the overall binding .... Your scientific idea are most
> welcome!!!
> Thanks in advance
> Best wishes
> Mahmoud
> --
> *************************************************
> Mahmoud E. Soliman
> Computational Chemistry & Modeling (PhD)
> Department of Chemistry
> University of Bath
> Bath
> BA2 7AY
> United Kingdom
> [1][2]http://people.bath.ac.uk/mess20/
> [2][3]http://www.bath.ac.uk/person/812559
> References
> 1. [4]http://people.bath.ac.uk/mess20/
> 2. [5]http://www.bath.ac.uk/person/812559
> _______________________________________________
> AMBER mailing list
> [6]AMBER.ambermd.org
> [7]http://lists.ambermd.org/mailman/listinfo/amber
>
> --
>
> *************************************************
>
> Mahmoud E. Soliman
>
> Computational Chemistry & Modeling (PhD)
>
> Department of Chemistry
>
> University of Bath
>
> Bath
>
> BA2 7AY
>
> United Kingdom
>
> [8]http://people.bath.ac.uk/mess20/
>
> [9]http://www.bath.ac.uk/person/812559
>
>
> *********************************************
>
> Mahmoud E. Soliman
>
> Lecturer of pharmaceutical organic chemistry
>
> Pharmaceutical Organic Chemistry Dept.
>
> Faculty of pharmacy
>
> Zagazig University
>
> Zagazig
>
> Egypt
>
> **********************************************
>
> Email:
>
> [10]mess20.bath.ac.uk
>
> [11]meelkot.zu.edu.eg
>
> [12]mahmoudelkot.gmail.com
>
> References
>
> 1. mailto:mahmoudelkot.gmail.com
> 2. http://people.bath.ac.uk/mess20/
> 3. http://www.bath.ac.uk/person/812559
> 4. http://people.bath.ac.uk/mess20/
> 5. http://www.bath.ac.uk/person/812559
> 6. mailto:AMBER.ambermd.org
> 7. http://lists.ambermd.org/mailman/listinfo/amber
> 8. http://people.bath.ac.uk/mess20/
> 9. http://www.bath.ac.uk/person/812559
> 10. mailto:mess20.bath.ac.uk
> 11. mailto:meelkot.zu.edu.eg
> 12. mailto:mahmoudelkot.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Mar 23 2011 - 08:00:03 PDT
