Thanks so much for your comments!
Best wishes
Mahmoud
On 4/18/11 5:53 PM, Carlos Simmerling wrote:
also make sure you are using Amber11 or later.
On Mon, Apr 18, 2011 at 11:51 AM, Ross Walker [1]<ross.rosswalker.co.uk> wrote:
Hi Mahmoud,
I wonder can I do NEB calculations to find the lowest energy path
between
two points (Reactant and product) for a reaction happens between a
ligand
and enzyme using QM/MM approach? or that would be difficult due the
fact
that in enzymes there will be thousands of degrees of freedom. If my
guess
is true, is there any alternative to do a simple QM/MM potential
energy
surface? any tutorial on that?
You can certainly do it the code will allow it. How well it will work will
very much depend on how you setup the calculation, the QM region you choose
and whether the QM theory model you use is appropriate for that reaction.
As
long as the bond is broken within the QM region though there is nothing
stopping you running this. You will just have to be careful building your
two end point prmtops. I suggest checking the literature for everything
involving NEB before you start though.
Good luck,
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| [2]
http://www.rosswalker.co.uk | [3]
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- [4]ross.rosswalker.co.uk |
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*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[9]
http://people.bath.ac.uk/mess20/
[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]mess20.bath.ac.uk
[12]meelkot.zu.edu.eg
[13]mahmoudelkot.gmail.com
References
1. mailto:ross.rosswalker.co.uk
2.
http://www.rosswalker.co.uk/
3.
http://www.wmd-lab.org/
4. mailto:ross.rosswalker.co.uk
5. mailto:AMBER.ambermd.org
6.
http://lists.ambermd.org/mailman/listinfo/amber
7. mailto: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:mess20.bath.ac.uk
12. mailto:meelkot.zu.edu.eg
13. mailto:mahmoudelkot.gmail.com
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Received on Mon Apr 18 2011 - 09:30:04 PDT
