Dear Bill,
So that I can run decomposition analysis using Amber 10 with mm_pbsa.pl? Am
I right?
Thanks
Best wishes
On 3/23/11 4:37 PM, Bill Miller III wrote:
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 [1]<mahmoudelkot.gmail.com>wr
ote:
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]
[2]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][3]
http://people.bath.ac.uk/mess20/
[2][3][4]
http://www.bath.ac.uk/person/812559
References
1. [4][5]
http://people.bath.ac.uk/mess20/
2. [5][6]
http://www.bath.ac.uk/person/812559
_______________________________________________
AMBER mailing list
[[7]6]AMBER.ambermd.org
[7][8]
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][9]
http://people.bath.ac.uk/mess20/
[9][10]
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:
[[11]10]mess20.bath.ac.uk
[[12]11]meelkot.zu.edu.eg
[[13]12]mahmoudelkot.gmail.com
References
1. [14]mailto:mahmoudelkot.gmail.com
2. [15]
http://people.bath.ac.uk/mess20/
3. [16]
http://www.bath.ac.uk/person/812559
4. [17]
http://people.bath.ac.uk/mess20/
5. [18]
http://www.bath.ac.uk/person/812559
6. [19]mailto:AMBER.ambermd.org
7. [20]
http://lists.ambermd.org/mailman/listinfo/amber
8. [21]
http://people.bath.ac.uk/mess20/
9. [22]
http://www.bath.ac.uk/person/812559
10. [23]mailto:mess20.bath.ac.uk
11. [24]mailto:meelkot.zu.edu.eg
12. [25]mailto:mahmoudelkot.gmail.com
_______________________________________________
AMBER mailing list
[26]AMBER.ambermd.org
[27]
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
[28]
http://people.bath.ac.uk/mess20/
[29]
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:
[30]mess20.bath.ac.uk
[31]meelkot.zu.edu.eg
[32]mahmoudelkot.gmail.com
References
1. mailto:mahmoudelkot.gmail.com
2. mailto:mahmoudelkot.gmail.com
3.
http://people.bath.ac.uk/mess20/
4.
http://www.bath.ac.uk/person/812559
5.
http://people.bath.ac.uk/mess20/
6.
http://www.bath.ac.uk/person/812559
7. mailto:6]AMBER.ambermd.org
8.
http://lists.ambermd.org/mailman/listinfo/amber
9.
http://people.bath.ac.uk/mess20/
10.
http://www.bath.ac.uk/person/812559
11. mailto:10]mess20.bath.ac.uk
12. mailto:11]meelkot.zu.edu.eg
13. mailto:12]mahmoudelkot.gmail.com
14. mailto:mahmoudelkot.gmail.com
15.
http://people.bath.ac.uk/mess20/
16.
http://www.bath.ac.uk/person/812559
17.
http://people.bath.ac.uk/mess20/
18.
http://www.bath.ac.uk/person/812559
19. mailto:AMBER.ambermd.org
20.
http://lists.ambermd.org/mailman/listinfo/amber
21.
http://people.bath.ac.uk/mess20/
22.
http://www.bath.ac.uk/person/812559
23. mailto:mess20.bath.ac.uk
24. mailto:meelkot.zu.edu.eg
25. mailto:mahmoudelkot.gmail.com
26. mailto:AMBER.ambermd.org
27.
http://lists.ambermd.org/mailman/listinfo/amber
28.
http://people.bath.ac.uk/mess20/
29.
http://www.bath.ac.uk/person/812559
30. mailto:mess20.bath.ac.uk
31. mailto:meelkot.zu.edu.eg
32. mailto:mahmoudelkot.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 23 2011 - 08:30:04 PDT
