Thanks Ross and sorry for being a bit hasty!
Best wishes
Mahmoud
On 5/6/11 1:15 PM, Ross Walker wrote:
Dear Mahmoud,
I wonder can Amber optimize TS for the QM region and calculate the
frequency
to make sure it has one imaginary frequency. I have a QM/MM PES
for
ligand-enzyme complex and I want to take the highest energy point
and
optimize it as a TS in the QM region, is it possible in Amber???
Unfortunately not right now. Firstly the minimizers in SQM are designed to
only go down hill and additionally there are not currently any second
derivatives to check the frequencies. If anybody wants to volunteer to add
these features we would be very grateful.
As another note I notice that you posted this question yesterday and then
you post the exact same question again just 11 hours later. Please do not do
this on the mailing. Be patient and eventually someone will answer your
question. Also take into account that it takes 24 hours for the sun to go
around the earth so at a minimum you should allow this amount of time for
people in the various time zones to read your email.
All the best
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 |
| [1]
http://www.rosswalker.co.uk | [2]
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- [3]ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
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[5]
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--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[6]
http://people.bath.ac.uk/mess20/
[7]
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:
[8]mess20.bath.ac.uk
[9]meelkot.zu.edu.eg
[10]mahmoudelkot.gmail.com
References
1.
http://www.rosswalker.co.uk/
2.
http://www.wmd-lab.org/
3. mailto:ross.rosswalker.co.uk
4. mailto:AMBER.ambermd.org
5.
http://lists.ambermd.org/mailman/listinfo/amber
6.
http://people.bath.ac.uk/mess20/
7.
http://www.bath.ac.uk/person/812559
8. mailto:mess20.bath.ac.uk
9. mailto:meelkot.zu.edu.eg
10. mailto:mahmoudelkot.gmail.com
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Received on Fri May 06 2011 - 04:30:04 PDT
