Re: [AMBER] TS calculation

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Fri, 06 May 2011 13:05:36 +0300

   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.





_______________________________________________
AMBER mailing list
[4]AMBER.ambermd.org
[5]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

   [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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 06 2011 - 04:30:04 PDT
Custom Search