yes, you'd want to use one standard angle, and one torsion angle. If the
cylinders are imagined to look like:
A'------------B'
--------X-------
A"-----------B"
C'-------------D'
--------Y--------
C"------------D"
Then you'd have:
Distance: X -> Y, which is your umbrella sampling reaction coordinate
Torsion: (C or D) -> Y -> X -> (A or B), and then fix this within a range
accordingly (e.g. if you choose C" -> Y -> X -> B", fix it to 180 degrees
+/- some amount)
Angle: C" -> Y -> X, and then fix this accordingly (e.g. for C" -> Y -> X,
you might also be choosing 0 or 180 degrees)
In this way, the torsion angle is what actually keeps the cylinders
parallel, and then the standard angle is what stops the now parallel
cylinders from rotating around one another.
Maybe that's all bogus, it's a lot of geometry.
~Aron
On Tue, Jan 15, 2013 at 4:00 PM, Elisa Frezza <elisa.frezza.gmail.com>wrote:
> Dear Adrian,
>
> you are right.
> When I use only an angular restraint my system are \ / at the end.
> Now I have to find the second angle for US, but it is not so easy.
>
> Thank you very much
>
> Elisa
>
>
> 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
>
> > Hi Eliza
> >
> > What I mean is that two cilinders can bet like this | |
> > or like this
> > \ /
> >
> > or one in the plane of the monitor and one NOT in the plane of the
> > monitor ;-)
> >
> > Hence, you need TWO angles to define the relative orientation between
> > two lines.
> >
> > adrian
> >
> > On 1/15/13 3:50 PM, Elisa Frezza wrote:
> > > Dear Adrian,
> > >
> > > Thank you very much for your answer and your opinion.
> > > Perhaps, I can consider only a restraint of distance, but I have to
> > wonder
> > > more carefully.
> > > I would like to ask you what kind of angle restraint do I have to use?
> > What
> > > do you mean with euler coordinates?
> > > I think to use torsional restraint, is it right? What do you suggest?
> > >
> > > Best regards
> > >
> > > Elisa
> > >
> > >
> > >
> > > 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> > >
> > >> Hi Eliza
> > >>
> > >> in that paper, the y present the PMF between DNA strands by "To this
> end
> > >> we added a restraint to the DNA oligomers
> > >> to bias them to sample the distance between their centers in a range
> of
> > >> 22 – 38 °A (smallest and
> > >> farthest separations, respectively). Several harmonic restraining
> > >> potentials have been put on both
> > >> DNA oligomers to ensure their approach in parallel orientation."
> > >>
> > >> This is quite simply totally wrong. You CANNOT do such a thing!
> > >>
> > >> At best, it would be a cut of a 2-D (or more) dimensional surface,
> with
> > >> biases that are not well defined. There is absolutely no reason to
> > >> believe that the approach between 2 DNA strands has them parallel to
> > >> each other in a minimum path sort of way.
> > >>
> > >> One more thing: to have two cylinders approaching each other in space,
> > >> requires one distance and TWO angles (euler coordinates), not just one
> > >> angle...
> > >>
> > >> adrian
> > >>
> > >> On 1/15/13 11:56 AM, Elisa Frezza wrote:
> > >>> Dear Rodrigo,
> > >>>
> > >>> I would like to study the PMF of a couple of DNA as reported in this
> > >>> article http://pubs.acs.org/doi/abs/10.1021/ja070207t
> > >>> I also would like to change the relative angle between the duplex.
> > >>> I do not care about change in DNA conformation
> > >>> I hope to have explain better my problem.
> > >>>
> > >>> Best regards
> > >>>
> > >>> Elisa
> > >>>
> > >>>
> > >>> 2013/1/15 ros <rodrigogalindo.gmail.com>
> > >>>
> > >>>> Hello Elisa!
> > >>>>
> > >>>> Depending on what you want to learn with your simulation, setting up
> > the
> > >>>> restraints for a double strand DNA can be very tricky. Consider that
> > if
> > >> you
> > >>>> set up more than one restraint, this will result in a multi
> > dimensional
> > >>>> sampling which will affect your results, as Prof. Roitberg pointed
> > out.
> > >> If
> > >>>> you are planning to use Prof. Grossfield WHAM implementation, this
> > code
> > >>>> will only do 2D sampling decomposition, so, for more than 2
> restraints
> > >> you
> > >>>> will have to write your own code or try to use other sampling
> > techniques
> > >>>> like mbar or Plumed.
> > >>>>
> > >>>> I am not sure what you are trying to do, but a dodecamer is a huge
> > >>>> molecule, so I would recommend that you start with a simple base
> pair
> > >> and
> > >>>> try different anchor points for your distance restraints (in my
> > >> experience,
> > >>>> C1', O1P, O2P or P are good starting points) and see what works.
> > >>>>
> > >>>> Finally, to capture the changes in the PES involving different
> > >> conformation
> > >>>> of DNA, I would recommend to use small windows (1 or even 0.5 A)
> which
> > >>>> results in a lot of computing time.
> > >>>>
> > >>>> Hope that helps!
> > >>>>
> > >>>> Rodrigo.
> > >>>>
> > >>>>
> > >>>> On Tue, Jan 15, 2013 at 9:05 AM, Elisa Frezza <
> elisa.frezza.gmail.com
> > >>>>> wrote:
> > >>>>> Dear Ross,
> > >>>>>
> > >>>>> Thank you very much.
> > >>>>>
> > >>>>> Best regards
> > >>>>>
> > >>>>> Elisa
> > >>>>>
> > >>>>>
> > >>>>> 2013/1/15 Ross Walker <ross.rosswalker.co.uk>
> > >>>>>
> > >>>>>> Dear Elisa et al,
> > >>>>>>
> > >>>>>> Please refer to the following webpage which maintains an up to
> date
> > >>>> list
> > >>>>>> of what is and isn't supported with the GPU code:
> > >>>>>>
> > >>>>>> http://ambermd.org/gpus/
> > >>>>>>
> > >>>>>> Specifically:
> > >>>>>>
> > >>>>>> 12) nmropt = 1 .and. For n=1,4; iat(n) < 0The GPU code does not
> > >>>> currently
> > >>>>>> support the use of COM simulations.
> > >>>>>>
> > >>>>>>
> > >>>>>> An update will be coming soon that will add Jarzynski support and
> > GBSA
> > >>>>>> support (as well as CUDA 5.0 and some additional bug fixes and
> > >> tweaks).
> > >>>>>> COM restraints are next on the list to be added but it may take a
> > >>>> while.
> > >>>>>> Until then I would suggest using pmemd.MPI running on CPUs which
> > >> should
> > >>>>>> support center of mass restraints.
> > >>>>>>
> > >>>>>> All the best
> > >>>>>> Ross
> > >>>>>>
> > >>>>>>
> > >>>>>> On 1/15/13 7:32 AM, "Elisa Frezza" <elisa.frezza.gmail.com>
> wrote:
> > >>>>>>
> > >>>>>>> I have tried, but it does not work, perhaps there are some
> mistakes
> > >> in
> > >>>>> my
> > >>>>>>> restraint file.
> > >>>>>>> My file is:
> > >>>>>>> #DNA
> > >>>>>>> #dna
> > >>>>>>> &rst iat=-1,-1,
> > >>>>>>> ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=100000,
> > >>>>>>> r1=0.0000E+00,r2=18.0000,r3=18.0000,r4=100.000,rk2=5,rk3=5,
> > >>>>>>> igr1 =
> > >>
> >
> 157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,181,182,18
> > >>>>>>> 3,185,18
> > >>
> >
> 8,189,190,191,192,193,196,198,199,201,202,204,205,209,210,211,213,214,215,
> > >>>>>>> 217,220,536,537,538,539,
> > >>
> >
> 540,543,545,546,548,549,551,552,553,554,557,558,560,561,562,564,567,568,56
> > >>>>>>> 9,570,571,572,575,577,57
> > >>>>>>> 8,580,581,583,584,588,589,590,594,596,599,
> > >>>>>>> igr2 =
> > >>
> >
> 915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,940,941,94
> > >>>>>>> 3,946,94
> > >>
> >
> 7,948,949,950,951,954,956,957,959,960,962,963,967,968,969,971,972,973,975,
> > >>>>>>> 978,1294,1295,1296,1297,
> > >>
> >
> 1298,1301,1303,1304,1306,1307,1309,1310,1311,1312,1315,1316,1319,1320,1322
> > >>>>>>> ,1325,1326,1327,1328,132
> > >>
> >
> 9,1330,1333,1335,1336,1338,1339,1341,1342,1346,1347,1348,1350,1351,1352,13
> > >>>>>>> 54,1357
> > >>>>>>> &end
> > >>>>>>>
> > >>>>>>> NOTE: I have not include angular restraint.
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> 2013/1/15 Aron Broom <broomsday.gmail.com>
> > >>>>>>>
> > >>>>>>>> is the COM restraint just not supported on GPU then? I was
> going
> > to
> > >>>>> try
> > >>>>>>>> and apply one myself on the PMEMD GPU version, and I had thought
> > >>>> that
> > >>>>>>>> was
> > >>>>>>>> one of the improvement for AMBER12. Have you tested your input
> > file
> > >>>>>>>> with
> > >>>>>>>> just PMEMD or even sander and confirmed that it works there and
> > just
> > >>>>> not
> > >>>>>>>> with pmemd.cuda?
> > >>>>>>>>
> > >>>>>>>> ~Aron
> > >>>>>>>>
> > >>>>>>>> On Tue, Jan 15, 2013 at 7:23 AM, Elisa Frezza <
> > >>>> elisa.frezza.gmail.com
> > >>>>>>>>> wrote:
> > >>>>>>>>> Dear Aron,
> > >>>>>>>>>
> > >>>>>>>>> thank you very much for your answer. I am using PMEMD GPU in
> > >>>>> AMBER12,
> > >>>>>>>> and I
> > >>>>>>>>> try to use COM restraint but it fails.
> > >>>>>>>>> It is quite difficult to explain you without a figure what I am
> > >>>>>>>> doing. If
> > >>>>>>>>> you want, I can write in your private email and I am trying to
> > >>>>> explain
> > >>>>>>>> you
> > >>>>>>>>> better.
> > >>>>>>>>>
> > >>>>>>>>> Thank you in advance
> > >>>>>>>>>
> > >>>>>>>>> Elisa
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> 2013/1/15 Aron Broom <broomsday.gmail.com>
> > >>>>>>>>>
> > >>>>>>>>>> 1) I believe you can indeed do a COM restraint (I assume you
> > >>>> mean
> > >>>>>>>> the
> > >>>>>>>>>> distance between multiple atoms center of mass?), it just
> > >>>> requires
> > >>>>>>>>> defining
> > >>>>>>>>>> groups, it should all be in the manual under the NMR
> refinement
> > >>>>>>>> section.
> > >>>>>>>>>> 2) For umbrella sampling, you can define say an angular
> > >>>> restraint
> > >>>>>>>> (or
> > >>>>>>>>>> several) to hold things in the orientation you want and then
> do
> > >>>>> the
> > >>>>>>>>>> umbrella sampling along just a distance. This will work and
> if
> > >>>>> not
> > >>>>>>>>>> uncommon, but you just have to be aware that the PMF you are
> > >>>>>>>> getting is
> > >>>>>>>>> for
> > >>>>>>>>>> that particular movement only. If you have good reason to
> think
> > >>>>>>>> that
> > >>>>>>>> is
> > >>>>>>>>>> the most energetically relevant movement (i.e. lowest free
> > >>>> energy
> > >>>>>>>> path)
> > >>>>>>>>>> then it is a fair assumption to make.
> > >>>>>>>>>>
> > >>>>>>>>>> ~Aron
> > >>>>>>>>>>
> > >>>>>>>>>> On Tue, Jan 15, 2013 at 7:11 AM, Elisa Frezza
> > >>>>>>>> <elisa.frezza.gmail.com
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>> Have you any suggestions?
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>> 2013/1/15 Elisa Frezza <elisa.frezza.gmail.com>
> > >>>>>>>>>>>
> > >>>>>>>>>>>> Dear Adrian,
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> thank you very much for your answer. I am using AMBER12 and
> > >>>> I
> > >>>>> am
> > >>>>>>>> not
> > >>>>>>>>>> sure
> > >>>>>>>>>>>> that I can use COM restraint.
> > >>>>>>>>>>>> At the same time, if I use only a distance restraint, my
> > >>>>>>>> molecules
> > >>>>>>>>>> start
> > >>>>>>>>>>>> to rotate and they are not parallel each other.
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> In conclusion, my question is: Can I put a lot of restraints
> > >>>>> and
> > >>>>>>>> then
> > >>>>>>>>>>>> consider only a distance between two atoms or is it not
> > >>>> right?
> > >>>>>>>>>>>> Elisa
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>> Elisa,
> > >>>>>>>>>>>>> Look at the Center of Mass restraints in the manual.
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> Also, if you want distance and angle PMF, you would need at
> > >>>>>>>> least
> > >>>>>>>> a
> > >>>>>>>>>> 2-D
> > >>>>>>>>>>>>> umbrella sampling scheme.
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> adrian
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> On 1/15/13 9:12 AM, Elisa Frezza wrote:
> > >>>>>>>>>>>>>> Dear All,
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> I am doing Umbrella Sampling on a pair of dodecamer and I
> > >>>>>>>> would
> > >>>>>>>>> like
> > >>>>>>>>>>> to
> > >>>>>>>>>>>>>> obtain the PMF as a function of the relative distance and
> > >>>>>>>>>> orientation.
> > >>>>>>>>>>>>>> I have noticed that I have to use a lot of restrains.
> > >>>>>>>>>>>>>> My question is:
> > >>>>>>>>>>>>>> is it right to put the restraint for each bond? Is it
> > >>>> right
> > >>>>>>>> to
> > >>>>>>>>>> obtain
> > >>>>>>>>>>>>> the
> > >>>>>>>>>>>>>> PMF?
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> My restraint files is like this:
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> #DNA
> > >>>>>>>>>>>>>> #dna
> > >>>>>>>>>>>>>> &rst
> > >>>>>>>>>>>>>> iat=62,820
> > >>>>>>>>>>>>>>
> > >>>>>>>> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > >>>>>>>>>>>>>> &end
> > >>>>>>>>>>>>>> &rst
> > >>>>>>>>>>>>>> iat=92,850
> > >>>>>>>>>>>>>>
> > >>>>>>>> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > >>>>>>>>>>>>>> &end
> > >>>>>>>>>>>>>> &rst
> > >>>>>>>>>>>>>> iat=125,883
> > >>>>>>>>>>>>>>
> > >>>>>>>> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> > >>>>>>>>>>>>>> &end
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> ......
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> thank you in advance
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>>> Elisa
> > >>>>>>>>>>>>>>
> > >>>>>>>>>>>>> --
> > >>>>>>>>>>>>> Dr. Adrian E. Roitberg
> > >>>>>>>>>>>>> Professor
> > >>>>>>>>>>>>> Quantum Theory Project, Department of
> > >>>>> Chemistry
> > >>>>>>>>>>>>> University of Florida
> > >>>>>>>>>>>>> roitberg.ufl.edu
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> _______________________________________________
> > >>>>>>>>>>>>> AMBER mailing list
> > >>>>>>>>>>>>> AMBER.ambermd.org
> > >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>> Elisa Frezza
> > >>>>>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > >>>>>>>>>>>> Dipartimento di Scienze Chimiche
> > >>>>>>>>>>>> Università di Padova
> > >>>>>>>>>>>> via Marzolo, 1
> > >>>>>>>>>>>> 35131 Padova - Italy
> > >>>>>>>>>>>> Phone: +39 049 827 5149
> > >>>>>>>>>>>> Skype: elisa.frezza
> > >>>>>>>>>>>> Emai: elisa.frezza.gmail.com
> > >>>>>>>>>>>> elisa.frezza.studenti.unipd.it
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>> --
> > >>>>>>>>>>> Elisa Frezza
> > >>>>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > >>>>>>>>>>> Dipartimento di Scienze Chimiche
> > >>>>>>>>>>> Università di Padova
> > >>>>>>>>>>> via Marzolo, 1
> > >>>>>>>>>>> 35131 Padova - Italy
> > >>>>>>>>>>> Phone: +39 049 827 5149
> > >>>>>>>>>>> Skype: elisa.frezza
> > >>>>>>>>>>> Emai: elisa.frezza.gmail.com
> > >>>>>>>>>>> elisa.frezza.studenti.unipd.it
> > >>>>>>>>>>> _______________________________________________
> > >>>>>>>>>>> AMBER mailing list
> > >>>>>>>>>>> AMBER.ambermd.org
> > >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>>>>
> > >>>>>>>>>>
> > >>>>>>>>>> --
> > >>>>>>>>>> Aron Broom M.Sc
> > >>>>>>>>>> PhD Student
> > >>>>>>>>>> Department of Chemistry
> > >>>>>>>>>> University of Waterloo
> > >>>>>>>>>> _______________________________________________
> > >>>>>>>>>> AMBER mailing list
> > >>>>>>>>>> AMBER.ambermd.org
> > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> Elisa Frezza
> > >>>>>>>>> Ph.D. Student in Materials Science and Engineering
> > >>>>>>>>> Dipartimento di Scienze Chimiche
> > >>>>>>>>> Università di Padova
> > >>>>>>>>> via Marzolo, 1
> > >>>>>>>>> 35131 Padova - Italy
> > >>>>>>>>> Phone: +39 049 827 5149
> > >>>>>>>>> Skype: elisa.frezza
> > >>>>>>>>> Emai: elisa.frezza.gmail.com
> > >>>>>>>>> elisa.frezza.studenti.unipd.it
> > >>>>>>>>> _______________________________________________
> > >>>>>>>>> AMBER mailing list
> > >>>>>>>>> AMBER.ambermd.org
> > >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>>
> > >>>>>>>>
> > >>>>>>>> --
> > >>>>>>>> Aron Broom M.Sc
> > >>>>>>>> PhD Student
> > >>>>>>>> Department of Chemistry
> > >>>>>>>> University of Waterloo
> > >>>>>>>> _______________________________________________
> > >>>>>>>> AMBER mailing list
> > >>>>>>>> AMBER.ambermd.org
> > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> Elisa Frezza
> > >>>>>>> Ph.D. Student in Materials Science and Engineering
> > >>>>>>> Dipartimento di Scienze Chimiche
> > >>>>>>> Università di Padova
> > >>>>>>> via Marzolo, 1
> > >>>>>>> 35131 Padova - Italy
> > >>>>>>> Phone: +39 049 827 5149
> > >>>>>>> Skype: elisa.frezza
> > >>>>>>> Emai: elisa.frezza.gmail.com
> > >>>>>>> elisa.frezza.studenti.unipd.it
> > >>>>>>> _______________________________________________
> > >>>>>>> AMBER mailing list
> > >>>>>>> AMBER.ambermd.org
> > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>
> > >>>>>> _______________________________________________
> > >>>>>> AMBER mailing list
> > >>>>>> AMBER.ambermd.org
> > >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>
> > >>>>>
> > >>>>> --
> > >>>>> Elisa Frezza
> > >>>>> Ph.D. Student in Materials Science and Engineering
> > >>>>> Dipartimento di Scienze Chimiche
> > >>>>> Università di Padova
> > >>>>> via Marzolo, 1
> > >>>>> 35131 Padova - Italy
> > >>>>> Phone: +39 049 827 5149
> > >>>>> Skype: elisa.frezza
> > >>>>> Emai: elisa.frezza.gmail.com
> > >>>>> elisa.frezza.studenti.unipd.it
> > >>>>> _______________________________________________
> > >>>>> AMBER mailing list
> > >>>>> AMBER.ambermd.org
> > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>
> > >>>> _______________________________________________
> > >>>> AMBER mailing list
> > >>>> AMBER.ambermd.org
> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>
> > >>>
> > >> --
> > >> Dr. Adrian E. Roitberg
> > >> Professor
> > >> Quantum Theory Project, Department of Chemistry
> > >> University of Florida
> > >> roitberg.ufl.edu
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> Università di Padova
> via Marzolo, 1
> 35131 Padova - Italy
> Phone: +39 049 827 5149
> Skype: elisa.frezza
> Emai: elisa.frezza.gmail.com
> elisa.frezza.studenti.unipd.it
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
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Received on Tue Jan 15 2013 - 13:30:03 PST