Dear Bill,
Thanks a lot.. Actually your comments have diverted my mind to a different
route in my project... I posted a new post regarding using PBSA on Amber 10,
you will see my post as well!!
Thanks
Mahmoud
On 3/23/11 3:53 PM, Bill Miller III wrote:
The Python version (MMPBSA.py) is a newer implementation of doing MM-PBSA
calculations for Amber simulations. The two programs will reproduce the same
binding energies given the same input values, despite the fact that they are
two different codes. There should be no problem with installing and running
MMPBSA.py on your cluster, except that you should be aware that the
decomposition analysis only works with Amber 11, as mentioned in the manual.
I hope that helps. Let us know if you have any other questions.
-Bill
On Wed, Mar 23, 2011 at 9:52 AM, Mahmoud Soliman [1]<mahmoudelkot.gmail.com>wro
te:
Hi all,
I am a new user to Amber and I am planning to do some MMPBSA binding
energy
for some enzyme-ligand complex. I went through the tutorial before I do
that
and I notice that the program uses Python scripts but on the cluster
(Amber
10 installed) that I am going to run the calculation on I see that it is
a
Perl script pbsa.pl. I wonder is there any technical difference between
pbsa.py and pbsa.pl I should be aware about before running the
calculations?
can I install the new version of MMPBSA on the cluster and still
compatible
with the Amber 10 version???
Any help would be appreciated....
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 - 07:30:04 PDT
