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&&使用amber跑带有金属离子的动力学如何做
使用amber跑带有金属离子的动力学如何做
如题，我要模拟的酶分子中含有金属镍离子，可是amber中没有设置金属镍离子的参数，其中有文献说，模拟过程中对镍离子选用non-bonded模型，具体参数设置如下：q=+2e．，σ=1.17 A，ε=0.100kcal/mol，即电荷为+2，离子范德华半径为1.17 A，势阱为0.100 kcal/mol。这个参数是怎么设置的，直接在pdb文件中没法设置啊，使用autodock或者amber怎么设置?求指教
是，top文件是参数文件，可是至少得生成top文件，貌似我在生成top文件时，就会报错，因为存在金属离子所以生不成top文件，难道是先不加载金属离子，生成top文件后在手动添加?额，让人头疼
你看的是哪个教程啊，我看的是amber tutorials，里面有个MCPB的，不过处理起来很麻烦，你可以给我发个教程的链接么，实在是太感谢了，多谢哈，
就是那个A1 Old
恩恩，找到了，万分感谢哈，我学学，我倒是会处理一些其他金属离子的了，因为知道他们的top文件，但是Ni还不是很会处理，看看这个方法行不行，多谢哈
学术必备与600万学术达人在线互动！
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英语翻译the old man saw some germans taking apart the amber roomand removing it you are talking to an old man
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扫描下载二维码From Wikipedia, the free encyclopedia
Pendants made of amber. The oval
is 52 by 32 mm (2.0 by 1.3 in).
An ant inside Baltic amber
was reconstructed using new amber from
National Archaeological Museum of Siritide to Matera
An amber violin , made by
in 1996/97.
Unpolished amber stones
Wood , the source of amber
Extracting Baltic amber from Holocene deposits, Gdansk, Poland
Unique colors of Baltic amber. Polished stones.
Fishing for amber on the coast of Baltic Sea. Winter storms throw out amber nuggets. Close to Gdansk, Poland.
tree , which has been appreciated for its color and natural beauty since
times. Much valued from antiquity to the present as a , amber is made into a variety of decorative objects. Amber is used in . It has also been used as a healing agent in folk medicine.
There are five classes of amber, defined on the basis of their chemical constituents. Because it originates as a soft, sticky tree resin, amber sometimes contains animal and plant material as . Amber occurring in coal seams is also called resinite, and the term ambrite is applied to that found specifically within
coal seams.
The English word amber derives from
?anbar ???? (cognate with
ambar) via
ambre. The word was adopted in
in the 14th century as referring to what is now known as
(ambre gris or "grey amber"), a solid waxy substance derived from the . In the , the sense of the word had come to be extended to Baltic amber (fossil resin) from as early as the late 13th century. At first called white or yellow amber (ambre jaune), this meaning was adopted in English by the early 15th century. As the use of ambergris waned, this became the main sense of the word.
The two substances ("yellow amber" and "grey amber") conceivably became associated or confused because they both were found washed up on beaches. Ambergris is less dense than water and floats, whereas amber is too dense to float, though less dense than stone.
The classical names for amber,
electrum and
(ēlektron), are connected to a term ?λ?κτωρ (ēlektōr) meaning "beaming ". According to myth, when
(the Sun) was killed, his mourning sisters became
trees, and their tears became elektron, amber.
Amber is discussed by
in the 4th century BC, and again by
(c. 330 BC) whose work "On the Ocean" is lost, but was referenced by , according to whose
(in what is also the earliest known mention of the name ):
Pytheas says that the , a people of Germany, inhabit the shores of an estuary of the Ocean called Mentonomon, their territory extending a distance of that, at one day's sail from this territory, is the Isle of , upon the shores of which, amber is thrown up by the waves in spring, it being an excretion of the se as, also, that the inhabitants use this amber by way of fuel, and sell it to their neighbors, the .
Earlier Pliny says that a large island of three days' sail from the
coast called
by , author of a fanciful travel book in Greek, is called Basilia by Pytheas. It is generally understood to be the same as Abalus. Based on the amber, the island could have been , , the shores of , the
or the , which were historically the richest sources of amber in northern Europe. It is assumed that there were well-established trade routes for amber connecting the Baltic with the Mediterranean (known as the ""). Pliny states explicitly that the Germans export amber to , from where it was traded further abroad by the . The ancient Italic peoples of southern Italy were working amber, the most important examples are on display at the National Archaeological Museum of Siritide to . Amber used in antiquity as at
and in the prehistory of the Mediterranean comes from deposits of .
Pliny also cites the opinion of , according to whom amber:
is a liquid produced by and that these rays, at the moment of the sun's setting, striking with the greatest force upon the surface of the soil, leave upon it an unctuous sweat, which is carried off by the tides of the Ocean, and thrown up upon the shores of Germany.
Besides the fanciful explanations according to which amber is "produced by the Sun", Pliny cites opinions that are well aware of its origin in tree resin, citing the native Latin name of succinum (sūcinum, from sucus "juice"). He writes:
Amber is produced from a marrow discharged by trees belonging to the pine genus, like gum from the cherry, and resin from the ordinary pine. It is a liquid at first, which issues forth in considerable quantities, and is gradually hardened [...] Our forefathers, too, were of opinion that it is the juice of a tree, and for this reason gave it the name of "succinum" and one great proof that it is the produce of a tree of the pine genus, is the fact that it emits a pine-like smell when rubbed, and that it burns, when ignited, with the odour and appearance of torch-pine wood.
He also states that amber is also found in Egypt and in India, and he even refers to the
properties of amber, by saying that "in Syria the women make the
of their spindles of this substance, and give it the name of harpax [from ?ρπ?ζω, "to drag"] from the circumstance that it attracts leaves towards it, chaff, and the light fringe of tissues."
Pliny says that the German name of amber was , "for which reason the Romans, when Germanicus Caesar commanded the fleet in those parts, gave to one of these islands the name of Glaesaria, which by the barbarians was known as Austeravia". This is confirmed by the recorded
for "amber" (c.f. ). In , amber was known as berne-, barn-, b?rnstēn. The Low German term became dominant also in
by the 18th century, thus modern German Bernstein besides Dutch
barnsteen.
term for amber is gintaras and
dzintars. They, and the
jantar or Hungarian gyanta ('resin'), are thought to originate from
jainitar ("sea-resin").[]
Early in the nineteenth century, the first reports of amber from North America came from discoveries in New Jersey along Crosswicks Creek near Trenton, at Camden, and near Woodbury.
in composition, but consists of several
bodies more or less soluble in ,
and , associated with an insoluble
substance. Amber is a
of several precursors in the
family, e.g. communic acid, cummunol, and biformene. These labdanes are
(C20H32) and trienes, equipping the organic skeleton with three
groups for . As amber matures over the years, more polymerization takes place as well as
reactions,
Heated above 200 °C (392 °F), amber decomposes, yielding an oil of amber, and leaves a black residue which is known as "amber colophony", or "amber pitch"; when dissolved in oil of
this forms "amber varnish" or "amber lac".
Molecular polymerization, resulting from high pressures and temperatures produced by overlying sediment, transforms the resin first into . Sustained heat and pressure drives off
and results in the formation of amber.
For this to happen, the resin must be resistant to decay. Many trees produce resin, but in the majority of cases this deposit is broken down by physical and biological processes. Exposure to sunlight, rain, microorganisms (such as bacteria and fungi), and extreme temperatures tends to disintegrate resin. For resin to survive long enough to become amber, it must be resistant to such forces or be produced under conditions that exclude them.
Amber from Bitterfeld
Fossil resins from Europe fall into two categories, the famous Baltic ambers and another that resembles the
group. Fossil resins from the Americas and Africa are closely related to the modern genus , while Baltic ambers are thought to be fossil resins from
family plants that used to live in north Europe.
Baltic amber with inclusions
The abnormal development of resin in living trees (succinosis) can result in the formation of amber. Impurities are quite often present, especially when the resin dropped onto the ground, so the material may be useless except for varnish-making. Such impure amber is called firniss.
of other substances can cause amber to have an unexpected color.
may give a bluish color. Bony amber owes its cloudy opacity to numerous tiny bubbles inside the resin. However, so-called black amber is really only a kind of .
In darkly clouded and even opaque amber, inclusions can be imaged using high-energy, high-contrast, high-resolution .
Amber mine "Primorskoje" in Jantarny, Kaliningrad Oblast, Russia
Amber is globally distributed, mainly in rocks of Cretaceous age or younger. Historically, the
coast west of
was the world's leading source of amber. The first mentions of amber deposits here date back to the 12th century. About 90% of the world's extractable amber is still located in that area, which became the
of Russia in 1946.
Pieces of amber torn from the seafloor are cast up by the waves, and collected by hand, dredging, or diving. Elsewhere, amber is mined, both in open works and underground galleries. Then nodules of blue earth have to be removed and an opaque crust must be cleaned off, which can be done in revolving barrels containing sand and water. Erosion removes this crust from sea-worn amber.
from Dominican Republic
, especially
, is mined through , which is dangerous due to the risk of tunnel collapse.
The Vienna amber factories, which use pale amber to manufacture pipes and other smoking tools, turn it on a
and polish it with whitening and water or with
and oil. The final luster is given by friction with flannel.
When gradually heated in an oil-bath, amber becomes soft and flexible. Two pieces of amber may be united by smearing the surfaces with , heating them, and then pressing them together while hot. Cloudy amber may be clarified in an oil-bath, as the oil fills the numerous pores to which the turbidity is due. Small fragments, formerly thrown away or used only for varnish, are now used on a large scale in the formation of "ambroid" or "pressed amber".
The pieces are carefully heated with exclusion of air and then compressed into a uniform mass by intense hydraulic pressure, the softened amber being forced through holes in a metal plate. The product is extensively used for the production of cheap jewelry and articles for smoking. This pressed amber yields brilliant interference colors in polarized light. Amber has often been imitated by other resins like
and , as well as by
and even . Baltic amber is sometimes colored artificially, but also called "true amber".
Amber occurs in a range of different colors. As well as the usual yellow-orange-brown that is associated with the color "amber", amber itself can range from a whitish color through a pale lemon yellow, to brown and almost black. Other uncommon colors include red amber (sometimes known as "cherry amber"), green amber, and even , which is rare and highly sought after.
Yellow amber is a hard fossil resin from evergreen trees, and despite the name it can be translucent, yellow, orange, or brown colored. Known to the Iranians by the Pahlavi compound word kah-ruba (from kah "straw" plus rubay "attract, snatch", referring to its electrical properties), which entered Arabic as kahraba' or kahraba (which later became the Arabic word for , ?????? kahrabā'), it too was called amber in Europe (Old French and Middle English ambre). Found along the southern shore of the Baltic Sea, yellow amber reached the Middle East and western Europe via trade. Its coastal acquisition may have been one reason yellow amber came to be designated by the same term as ambergris. Moreover, like ambergris, the resin could be burned as an incense. The resin's most popular use was, however, for ornamentation—easily cut and polished, it could be transformed into beautiful jewelry. Much of the most highly prized amber is transparent, in contrast to the very common cloudy amber and opaque amber. Opaque amber contains numerous minute bubbles. This kind of amber is known as "bony amber".
Although all
is fluorescent, the rarest Dominican amber is blue amber. It turns blue in natural sunlight and any other partially or wholly
light source. In long-wave UV light it has a very strong reflection, almost white. Only about 100 kg (220 lb) is found per year, which makes it valuable and expensive.
Sometimes amber retains the form of drops and , just as it exuded from the ducts and receptacles of the injured trees. It is thought that, in addition to exuding onto the surface of the tree, amber resin also originally flowed into hollow cavities or cracks within trees, thereby leading to the development of large lumps of amber of irregular form.
Amber can be classified into several forms. Most fundamentally, there are two types of plant resin with the potential for fossilization. , produced by conifers and angiosperms, consist of ring structures formed of
(C5H8) units.
are today only produced by , and tend to serve functional uses. The extinct
produced a third type of resin, which is often found as amber within their veins. The composition of resin each species produces a unique blend of chemicals which can be identified by the use of pyrolysis–gas chromatography–mass spectrometry. The overall chemical and structural composition is used to divide ambers into five classes. There is also a separate classification of amber gemstones, according to the way of production.
This class is by far the most abundant. It comprises labdatriene carboxylic acids such as communic or ozic acids. It is further split into three sub-classes. Classes Ia and Ib utilize regular labdanoid diterpenes (e.g. communic acid, communol, biformenes), while Ic uses enantio labdanoids (ozic acid, ozol, enantio biformenes).
Includes Succinite (= 'normal' Baltic amber) and Glessite. Have a communic acid base. They also include much succinic acid.
yields on dry distillation succinic acid, the proportion varying from about 3% to 8%, and being greatest in the pale opaque or bony varieties. The aromatic and irritating fumes emitted by burning amber are mainly due to this acid. Baltic amber is distinguished by its yield of succinic acid, hence the name succinite. Succinite has a hardness between 2 and 3, which is rather greater than that of many other fossil resins. Its specific gravity varies from 1.05 to 1.10. It can be distinguished from other ambers via
due to a specific
absorption peak. IR spectroscopy can detect the relative age of an amber sample. Succinic acid may not be an original component of amber, but rather a degradation product of abietic acid.
Like class Ia ambers, these are ba however, they lack .
This class is mainly based on enantio-labdatrienonic acids, such as ozic and zanzibaric acids. Its most familiar representative is Dominican amber.
Dominican amber differentiates itself from
by being mostly transparent and often containing a higher number of
inclusions. This has enabled the detailed reconstruction of the ecosystem of a long-vanished tropical forest. Resin from the extinct species
is the source of Dominican amber and probably of most amber found in the tropics. It is not "" but "".
These ambers are formed from resins with a sesquiterpenoid base, such as .
These ambers are .
Class IV is someth its ambers are not polymerized, but mainly consist of cedrene-based sesquiterpenoids.
Class V resins are considered to be produced by a pine or pine relative. They comprise a mixture of diterpinoid resins and n-alkyl compounds. Their main variety is .
Typical amber specimen with a number of indistinct inclusions
The oldest amber recovered dates to the
period ( million years ago). Its chemical composition makes it difficult to match the amber to its producers – it is most similar to the however, there are no flowering plant fossils until the Cretaceous, and they were not common until the . Amber becomes abundant long after the Carboniferous, in the ,  million years ago, when it is found in association with . The oldest amber with arthropod inclusions comes from the Levant, from Lebanon and Jordan. This amber, roughly 125–135 million years old, is considered of high scientific value, providing evidence of some of the oldest sampled .
In Lebanon, more than 450 outcrops of Lower Cretaceous amber were discovered by Dany Azar, a Lebanese paleontologist and entomologist. Among these outcrops, 20 have yielded biological inclusions comprising the oldest representatives of several recent families of terrestrial arthropods. Even older,
amber has been found recently in Lebanon as well. Many remarkable insects and spiders were recently discovered in the amber of Jordan including the oldest , , umenocoleid , and achiliid .
Baltic amber or succinite (historically documented as Prussian amber) is found as irregular
sand, known as blue earth, occurring in the Lower
(in historical sources also referred to as Glaesaria). After 1945, this territory around
was turned into , , where amber is now systematically mined.
It appears, however, to have been partly derived from older
deposits and it occurs also as a derivative phase in later formations, such as . Relics of an abundant flora occur as inclusions trapped within the amber while the resin was yet fresh, suggesting relations with the flora of Eastern
and the southern part of .
named the common amber-yielding pine of the Baltic forests Pinites succiniter, but as the wood does not seem to differ from that of the existing genus it has been also called Pinus succinifera. It is improbable, however, that the production of amber was limited and indeed a large number of conifers belonging to different genera are represented in the amber-flora.
Amber is a unique , preserving otherwise unfossilizabl as such it is helpful in the reconstruction of ecosystems
the chemical composition of the resin, however, is of limited utility in reconstructing the phylogenetic affinity of the resin producer.
Amber sometimes contains animals or plant matter that became caught in the resin as it was secreted. Insects, spiders and even their webs, annelids, frogs, crustaceans,
and , marine microfossils, wood, flowers and fruit, hair, feathers and other small organisms have been recovered in Cretaceous ambers (deposited c.  million years ago). The oldest amber to bear fossils (mites) is from the Carnian (Triassic,  million years ago) of north-eastern Italy.
Amber has been used since prehistory () in the manufacture of jewelry and ornaments, and also in .
Amber has been used as jewelry since the Stone Age, from 13,000 years ago. Amber ornaments have been found in
tombs and elsewhere across Europe. To this day it is used in the manufacture of smoking and glassblowing mouthpieces. Amber's place in culture and tradition lend
is dedicated to the fossilized resin.
Amber has long been used in
for its purported healing properties. Amber and extracts were used from the time of
in ancient
for a wide variety of treatments through the
and up until the early twentieth century.[]
Lithuanian amber jewelry
In , it was customary to burn amber during large festivities. If amber is heated under the right conditions,
is produced, and in past times this was combined carefully with
to create "artificial musk" – a resin with a peculiar
odor. Although when burned, amber does give off a characteristic "pinewood" fragrance, modern products, such as , do not normally use actual amber due to the fact that fossilized amber produces very little scent. In perfumery, scents referred to as “amber” are often created and patented to emulate the opulent golden warmth of the fossil.
The modern name for amber is thought to come from the
word, ambar, meaning . Ambergris is the waxy aromatic substance created in the intestines of
and was used in making perfumes both in ancient times as well as modern.
The scent of amber was originally derived from emulating the scent of ambergris and/or
but due to the
status of the sperm whale the scent of amber is now largely derived from labdanum. The term “amber” is loosely used to describe a scent that is warm, musky, rich and honey-like, and also somewhat earthy. It can be synthetically created or derived from natural resins. When derived from natural resins it is most often created out of labdanum.
is usually part of the recipe.
are sometimes used to enhance the aroma.
"Amber" perfumes may be created using combinations of labdanum, ,
(itself a type of tree resin used in incense manufacture), vanilla,
and/or synthetic materials.
Young resins, these are used as imitations:
Kauri resin from
trees in New Zealand.
( resins). The African and American () copals from
trees family (genus ).
or Mexican type ( of fossil resins). Copals from Manilia () and from New Zealand from trees of the genus
Other fossil resins:
Other natural resins —
Plastics, these are used as imitations:
(inorganic material) and other
(obtain first time in 1833) — a product of treatment of cellulose with nitration mixture.
Acetylcellulose (not in the use at present)
or "artificial horn" (condensation product of casein and formaldehyde), other trade names: Alladinite, Erinoid, Lactoid.
— a conjugated protein forming from the casein precursor – caseinogen.
Resolane (phenolic resins or phenoplasts, not in the use at present)
resine (resol, phenolic resins), product from
are known under the misleading name "African amber".
resins — , formaldehyde and urea-formaldehyde resins.
(phenolic resins), unofficial name "antique amber", not in the use at present
(Polish amber imitation) with . Ex.: unsaturated polyester resins (polymals) are produced by Chemical Industrial Works "" in , ; estomal are produced by
firm. Polybern or sticked amber is artificial resins the curled chips are obtained, whereas in the case of amber – small scraps. "African amber" (polyester, synacryl is then probably other name of the same resine) are produced by R Styresol trade mark or alkid resin (used in Russia, Reichhold, Inc. patent, 1948.
and polystyrene-like polymers ().
(), especially
(trade mark Plexiglass, metaplex).
Jessamyn Reeves-Brown (November 1997). . Strings (65). Archived from
on 14 May .
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Harper, Douglas. . . and .
(3rd ed.). . September 2005. (Subscription or
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see: Abu Zaid al Hassan from Siraf & Sulaiman the Merchant (851), Silsilat-al-Tawarikh (travels in Asia).[]
( 6.513, 19.398). The feminine ?λεκτρ?? being later used as a name of the . King, Rev. C.W. (1867). . Cambridge (UK). p. 315.
The derivation of the modern term "" from the Greek word for amber dates to the 1600 ( electricus "amber-like", in De Magnete by ). Heilbron, J.L. (1979). . University of California Press. p. 169.  .. The word "" (for the fundamental particle) was coined in 1891 by the Irish physicist
whilst analyzing elementary charges for the first time. Aber, Susie Ward. . Emporia State University.
from the original on 28 April .. .
Michael R. Collings, Gemlore: An Introduction to Precious and Semi-Precious Stones, 2009, p. 20
Natural History .
Natural History
or IV.13.95 in the Loeb edition.
as well as succinite, a term given to a particular type of amber by
Manuel Villanueva-García, Antonio Martínez-Richa, and Juvencio Robles
(EJ-1567C) pp. 449–458
Rice, Patty C. (2006). Amber: Golden Gem of the Ages. 4th Ed. AuthorHouse.  .
Poinar, George O. (1992) Life in amber. Stanford, Calif.: Stanford University Press, p. 12,  
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Sherborn, Charles Davies. .
Amos, Jonathan (1 April 2008). . BBC News.
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, Ambery.net
6 July 2012 at the .. Gurukul.ucc.american.edu. Retrieved on 19 September 2012.
Wichard, Wilfred and Weitschat, Wolfgang (2004) Im Bernsteinwald. – Gerstenberg Verlag, Hildesheim,  
"Amber". (1999). In G. W. Bowersock, Peter Brown, Oleg Grabar (eds.) Late Antiquity: A Guide to the Postclassical World, Harvard University Press,  .
Manuel A. Iturralde-Vennet (2001).
(PDF). Caribbean Journal of Science. 37 (3): 141–167. Archived from
(PDF) on 11 May 2011.
Anderson, K; Winans, R; Botto, R (1992). "The nature and fate of natural resins in the geosphere—II. Identification, classification and nomenclature of resinites". Organic Geochemistry. 18 (6): 829–841. :.
Anderson, K; Botto, R (1993). "The nature and fate of natural resins in the geosphere—III. Re-evaluation of the structure and composition of Highgate Copalite and Glessite". Organic Geochemistry. 20 (7): 1027. :.
Anderson, Ken B. (1996). "New Evidence Concerning the Structure, Composition, and Maturation of Class I (Polylabdanoid) Resinites". Amber, Resinite, and Fossil Resins. ACS Symposium Series. 617. pp. 105–129. :.  .
Shashoua, Yvonne (2007).
(PDF). Department of Conservation, The National Museum of Denmark. Archived from
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George Poinar, Jr. and Roberta Poinar, 1999. The Amber Forest: A Reconstruction of a Vanished World, (Princeton University Press)  
Grimaldi, D. A. (1996) Amber – Window to the Past. – American Museum of Natural History, New York,  
Bray, P. S.; Anderson, K. B. (2009). "Identification of Carboniferous (320 Million Years Old) Class Ic Amber". Science. 326 (5949): 132–134. :. :.  .
Poinar, P.O., Jr., and R.K. Milki (2001) Lebanese Amber: The Oldest Insect Ecosystem in Fossilized Resin. Oregon State University Press, Corvallis.  .
Azar, Dany (2012). "Lebanese amber: a "Guinness Book of Records"". Annales Universitatis Paedagogicae Cracoviensis. 111: 44–60.
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