Dear Thomas,
Actually your reply to Catherine has encouraged me to seek your advice about
my case: I need to do a PMF for some reaction coordinate (nucleophilic
attack) using QM/MM facility in Amber 10. I read through steered MD
simulation but it sounds to me (from the comments I get from Amber
users/developers) that SMD is a bit doggy and some people getting some
trouble to publish work with SMD. Is there any EASY and reliable alternative
in Amber 10 that I can apply to do a PMF for NU or PT reactions in enzyme???
do you have any tutorial/example for the methode you explain below to
Catherine that I can use??
Best wishes
Mahmoud
On 3/24/11 5:04 PM, [1]steinbrt.rci.rutgers.edu wrote:
Hi,
I am not sure if this is what you mean, but if you can define a clear
reaction coordinate x for the change you see, e.g. some distance, you can
use ptraj to analyse the time series of movement along it, compute a
histogram P(x) and transform it into a potential of mean force via dF=
-RTln P(x). This is only meaningful if all points along x are well sampled
though.
Kind Regards,
Thomas
On Thu, March 24, 2011 10:55 am, Catein Catherine wrote:
Dear Sir/Madam,
I have done the MD simulations. I would like to analysis the free energy
landscapes of a conformational change during a long MD simulations.
Can I do it with ptraj or any other softwares or scripts?
Best regards,
Catherine
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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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. mailto:steinbrt.rci.rutgers.edu
2. mailto:AMBER.ambermd.org
3.
http://lists.ambermd.org/mailman/listinfo/amber
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 Thu Mar 24 2011 - 08:30:04 PDT
