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Title

The Amber Molecular Dynamics Package

Description

Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids

Keywords

molecular dynamics,proteins,nucleic acids,biomolecular simulation,Peter Kollman,David Case

H1

AmberTools13 is now available!
Amber12 is now available!

H2

News
Quick links
Assisted Model Building with Energy Refinement
General information
Code overview
Benchmarks
Downloads
Amber-related links
The force field
How to obtain the Amber12 program package
General correspondence
The AMBER Mail Reflector
Amber developers

H3

Tips for installing and running Amber on various architectures
Updated information about various components
Visualizing Amber structures and trajectories
Related software that interfaces with Amber
More information about Amber force fields
Using the Amber force field in other software packages

H4

H5

Text Analysis

Cloud of Keywords from all content
High relevance
 

amber field molecular ambertools dynamics programs program fields simulations reflector analysis code gpu ambertools13 sander running version walker software models amber12 package pmemd support calculations cheatham pdf case license developers file wang general simmerling tutorials features merz card poisson-boltzmann people archive developed university the amber users trajectories leap download protein free based distributed credit solvent update including molecules

Medium relevance
 

source versions april order photo restraints chem packages directory suite includes rutgers energy carry files iii tool reference manual questions codes duke quantum swails tree installation designed interface structures process modeling systems wong antechamber proteins nmr brook subscribers mcpb nvidia numerical generalized ptraj originally born payment consists california work authors cpptraj francisco agreement andreas accelerated kollman acids untar updated variety hardware amber10 benchmarks expanded amber-aware salomon-ferrer overview public simulation documentation tools visualization major instructions release examples building model darden improved meeting updates potentials energies ff99sbildn prepared timings lists nucleic benchmark released gtz gromacs roitberg gohlke scripts kepler windows automate cieplak

Low relevance
 

designed interface structures process modeling systems wong antechamber proteins nmr brook subscribers mcpb nvidia numerical generalized ptraj originally born payment consists california work authors cpptraj francisco agreement andreas accelerated kollman acids untar updated variety hardware amber10 benchmarks expanded amber-aware salomon-ferrer overview public simulation documentation tools visualization major instructions release examples building model darden improved meeting updates potentials energies ff99sbildn prepared timings lists nucleic benchmark released gtz gromacs roitberg gohlke scripts kepler windows automate cieplak ambermd secure and replica exchange listinfo script type periodic types mailman information only sampling amber@ambermd enchanced upgrade ideas correspondence compatible nicole administrative eligible february account version 11 of the http lipid fax automatic phone differences click energetics newer version 1 separate amber11 mtkpp mike details link thorsten sdsc wlfle loeffler july database bz2 installing prepare wham esp charge protonation dupradeau charges remd mm-pbsa acpype ubuntu jason older group dave modifications ff99sb faq asked money licensing chemical functions justification japanese integration included replica-exchange orders description groups pmf bob input namd residues pdb analyze assist command charmm academic scales fees copy force field builder gpus theft kovalenko gusarov diego ray carlos luchko babin roe mathews seetin sagui build distance performs chemistry integral join structure basic metal 3d-rism community create organic cai steinbrecher biomolecular simulation domain row molecular dynamics left georgia patch manuals k20 recommended acceleration cite zhang vanicek wolf liu brozell paesani kolossvry roberts hayik seabra goetz amberlite hsieh compilers pbsa mmpbsa compiled licenses options distribution in order

Very Low relevance
 
ambermd secure and replica exchange listinfo script type periodic types mailman information only sampling amber@ambermd enchanced upgrade ideas correspondence compatible nicole administrative eligible february account version 11 of the http lipid fax automatic phone differences click energetics newer version 1 separate amber11 mtkpp mike details link thorsten sdsc wlfle loeffler july database bz2 installing prepare wham esp charge protonation dupradeau charges remd mm-pbsa acpype ubuntu jason older group dave modifications ff99sb faq asked money licensing chemical functions justification japanese integration included replica-exchange orders description groups pmf bob input namd residues pdb analyze assist command charmm academic scales fees copy force field builder gpus theft kovalenko gusarov diego ray carlos luchko babin roe mathews seetin sagui build distance performs chemistry integral join structure basic metal 3d-rism community create organic cai steinbrecher biomolecular simulation domain row molecular dynamics left georgia patch manuals k20 recommended acceleration cite zhang vanicek wolf liu brozell paesani kolossvry roberts hayik seabra goetz amberlite hsieh compilers pbsa mmpbsa compiled licenses options distribution in order field more fields glycam prabal piotr maiti parameters glycam for sander modified nucleosides john santalucia inputs web-based polymer luo back input configurator for carbohydrates amber dendrimer simon island meetings participants tools for francisco 600 2280 university gilson additional diffusion peter bilayer hannes kennie residence crowley junmei tom darden 16th toolkit caldwell joint in stony 522 san october amber developers held has entries commonly older photo requested crew piana palmo maragakis 502-6518 fax lindorff-larsen 94158-2517 phone of peter to ff99sb biochemistry co-factor pang reddb data jim yuan-ping wayne photos zinc parameters base room fragments and co-workers projects biological november libraries small molecules and berny schlegel accent-mm contact umbrella daniel sindhikara these contributions histogram analysis alan grossfield weighted feb sane duggan sietraj is an amber amber brendan list helped interfacing processing is a outlined to estimate pka chains modified of structural common of conformations massaging carrying administrator ccb of assigning another tool graduate assign play pdb2pqr documentation last reading takesono alternative author topologies 2010 athens 2009 stony compounds 2011 rutgers generate apbs 2012 salt on python to interface python bat-values 514-1546 email island extract amber2accent applications ccpn aria solver adaptive poisson-boltzmann plugins with other notes the ryde package contains plumed calculating binding from amber-generated listed illustrate pbsa scripts city lake iapbs interface entropies 2013 the method for estimating simon side-chain torsion delays north america western europe researchers are generally required s main waivers japan waiver online prior shipment obtaining must received to amber-admin@biomaps before sending payment details in receiving chemistry@ccl developers amber is paid fortran development active institutions employ some collaboration will also and since lot encouraged to addressed special circumstances waived install fee reduced via check amber-admin@biomaps reflector address ensemble and search distribute consult reflector only unjoin longer accepted reflectors licensed items you wish submit discussed for a box google reflector using queries transfers american express discussion visa mastercard to the announcements amber-specific issues problems payments e-mail amber to wire purchase plain text interpreting regents of david funds accelrys flowers amber amberffc gaussian of manchester using exists richard subscribed bryce forwarded forum ffamber x-plor using amber force scientific bugfixes discussions on the uiuc subscribe maintained your $amberhome leaprc ff99sbnmr force to amber-subscribe@ambermd indicating klepeis dror shaw nicole@picasso ucsf nmr-based angew contributed parameters bruschweiler blank torsional see d edu do molden desmond for-profit florida and adrian industrial $400 flowers non-profit government $20 licensees at the case at agreement for demonstration porting utah $15 for licensees at suny-stony posting package click print return moe leadership preliminary address below openmm using southwestern address junmei wang bound irvine purchase a receive the bottom electronically processed additional information outperform lipid11 modular pairwise additive solvation calculations polarizable ff12sb happy represents include fixed-charge membrane periodic systems aqueous electrolytes self-guided langevin treatement with a equation model kovalenko-hirata closure approximations reference manual download ambertools13 inspecting modifying amber parameter ambertools12 gb models access greatly analyzing trajectories solvers and dielectric to download simply re-run configure re-compile user --upgrade finish --update your amberhome patch-level may have enchance soft cryo em experiments constraints rigid maps density disappearing atoms tighter facilities electron partially flexible bug easily question answered formats code linked engine fixes english introduction frequently appearing procedures of hamiltonian am1 pm6 external allowing d-orbitals degrees freedom simplified semi-empirical chemistry programs expanding k10 gtx6xx methods change hamiltonian latest nmropt cpu including temperature isotropic harmonic meet the manual woods computat 1668-1688 protein force onufriev 198-210 versa good wires sci be found ponder promise biopolymers 232-256 mark limitations successes adv 27-85 for nucleic young you can parts sep released quick links amber fields amber-related announced workstations learn contacts developers news k20x links benchmarks gpu support file biomolecules are in used in of molecular simulation mechanical force refers formats ordering amber12 mailing lists assisted energy refinement williamson dong equation solvation mdgx explicit simulations ptraj solves models 3d-rism semiempirical dftb program pbsa solutions trajectories mmpbsa energy-based are included open-source fortran90 also you components gpl analyses trajectories the mostly released gnu simulations sqm preparation microsecond theory 1542-1555 ct200909j amber routine walker* duncan poole scott grand january custom geometry implicit models antechamber centers tleap water either explicit independently well by complete mdgx overview the well together library mtk own programs $amberhome for instance illustrative as well this is untar this in amber11 in a jxvf $amberhome amber-related debian opensuse ibm bluegene macosx linux links tips architectures running fedora suse follow the atoms benchmarked downloads old prep edit counts outperforms other lammps or namd addendum typically parm spasms romanovski cellulose on a largish vladimir widget molecular dynamics charge-fitting q&a the xraw sun scott brozell helicoidal plots from amber interfaces teletchea stephane pcasuite principal component plotting tools amber r derive calculations with facilitates amber tasks dealing mmtsb biology calculating resp pigache multiscale in structural aka quasiharmonic essential cards e-nmr european grid vasilyev vladislav microsoft on running fujitsu primepower vpp components more module details viewer visual vmd package chimera interactive essential dynamics trajectory lightweight set of evb visualizing trajectories md display size counts regardless well-tested fashion high-performance environments named most-used features implements vehicle explore and pmemd production acid specialized integral-equation study protein-ligand interaction rism distance-geometry language writing manipulate mechanics we are starting angle penalty shifts noesy torsion noe-derived simulated annealing nmr-derived refinement volumes thermodynamic faster parallel machines additionally gb simulations pme capability extensively-modified the sander optimized x-windows-based coordinate collection represent typical usage benchmarks benchmark basins pieces arising estimate conformational benchmarks from daresbury fares smaller sizes may even report quoting comparing number wynn march 2012 break continuum developing descriptors starts generates automates manipulating parameter topology creation editor generated generating time-correlation diffusional behavior post-processing bonding hydrogen centers computing rms deviation consistent

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amber

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package

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package amber12 software general proteins field links dynamics

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amber12 software general proteins field links dynamics architectures updated components running peter kollman installing david case tips visualizing nucleic acids fields packages interfaces developers structures trajectories biomolecular simulation molecular dynamics amber-related acids ambertools13 news nucleic simulations molecular programs for molecular assisted model downloads program correspondence benchmarks overview building energy refinement code reflector