You can do umbrella sampling in amber using restraints
I do not think we have a tutorial for that, but if you read on umbrella
in general, it should be simple to see how you use restraint potentials
to do it in amber.
Adrian
On 3/24/11 4:23 PM, Mahmoud Soliman wrote:
>
> 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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> [2]AMBER.ambermd.org
> [3]http://lists.ambermd.org/mailman/listinfo/amber
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> 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. 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Thu Mar 24 2011 - 08:30:06 PDT
