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
Received on Wed Mar 23 2011 - 08:00:02 PDT
