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     1  ~ 2014 sep 27moilviewRe: [AMBER] MOIL-view alternatives - amber mailing list archive2011/2/4 Carlos Simmerling <carlos.simmerling.gmail.com> > moil-view was only available for SGI workstations. You can check Amber > ptraj ...
     2  ~ 2014 sep 23amberThe Amber Molecular Dynamics PackageAmber is a package of programs for molecular dynamics simulations of proteins and nucleic acids.
     5  +1 2014 sep 12gpu accelerated applicationAmber (PMEMD) NVIDIA GPU SupportSupport for NVIDIA GPU acceleration of AMBER PMEMD Calculations by Ross C .
     6  +2 2014 jul 23amber with bugAMBER Bug Fixes and UpdatesAMBER Bug Fixes and Updates. These pages include both traditional "bug fixes", along with various updates, such as Machine files for new compilers or ...
     7  +1 2014 sep 27gpu benchmarkAMBER GPU BenchmarksBenchmarks for the GPU accelerated version of the AMBER Molecular Dynamics Code.
     7  -1 2014 sep 06gpu benchmarks
     8  +1 2014 sep 19snapshot vmdRe: [AMBER] Trivial VMD question - amber mailing list archiveI think that's needed for snapshot in VMD to work. Good luck! Jason On Wed, Sep 1, 2010 at 12:46 PM, <steinbrt.rci.rutgers.edu> wrote: > Hi, >
     9  +49 2014 aug 16gpu computing informationEarly on within the mdout file you will find information on the GPU being used ..... ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU -Util Compute M.
     10  ~ 2014 sep 10namdUsing the Amber force field in NAMDNAMD , on the other hand, continues to scale well at 256 threads and beyond. Hence, if you have access to large numbers of nodes in a ...
     11  -2 2014 aug 11structural entropy pdb softwareAmber Advanced Tutorials - Tutorial 3 - MMPBSA.py - Section 51) Build the starting structure and run a simulation to obtain an equilibrated system. ... Here is a pre-prepared pdb file of the complex. ... general section to perform a Quasi-Harmonic entropy calculation using the ptraj program in AmberTools.
     12  -4 2014 sep 20myunggi universityRe: AMBER: reference of ff99 from Myunggi Yi on 2006-08-31 On 8/31/06, Myunggi Yi < myunggi .gmail.com> wrote: ... Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: ...
     13  +1 2014 jul 27uni hamburg chemieRe: [AMBER] binding energy calculation problem from poll. chemie From : <poll. chemie . uni - hamburg .de> Date : Thu, 24 Feb 2011 11:27:28 +0100. Hi everybody, so finally I get MMPBSA.py to work.
     14  +19 2014 aug 28conversion key xtcRe: [AMBER] conversion of gromacs trajectory file ( xtc ) to amber Re: [AMBER] conversion of gromacs trajectory file ( xtc ) to amber trajectory file ( mdcrd) / problem in ... gromacs file) of this key water molecule.
     16  +14 2014 sep 03bugs in amberAmberTools Bug Fixes and UpdatesNote: The individual bug fixes for AmberTools are described below in case you ... update.5: Fix a number of small bugs in PBSA that were patched in previous ...
     16  +15 2014 aug 20san francisco self force"Amber" refers to two things: a set of molecular mechanical force fields for the
     19  -1 2014 sep 16turn off cudaJarzynski Sampling; GBSA support; Support for off -diagonal modifications to VDW .... GPU accelerated PMEMD has been implemented using CUDA and thus will .... the GPU's available memory is reduced by 1/9th if you have ECC turned on.
     19  ~ 2014 sep 02development and testingDevelopment and testing of a general amber force fieldDevelopment and Testing of a General Amber Force Field. JUNMEI WANG,1 ROMAIN M. WOLF,2 JAMES W. CALDWELL,. PETER A. KOLLMAN, DAVID A.
     20  -6 2014 sep 18ccl ccg[AMBER-Developers] CCL : Chemical Computing Group Announces From : case <case.biomaps.rutgers.edu> Date : Fri, 18 Mar 2011 17:22:50 -0400. On Fri, Mar 18, 2011, Shirley Peng speng/achemcomp.com ...
     21  -7 2014 sep 10install x window cygwinRunning Amber on Microsoft WindowsGeneral remarks | Installation on Windows using Cygwin | ... (including the X - windows parts) will compile and run on Windows using the Cygwin development  ...
     22  ~ 2014 sep 09lg ca 479 ubaAmber 11 Users‛ ManualMerck-Frosst, Canada for permission to include charge increments for the AM1- BCC charge scheme.
     23  +13 2014 sep 17bmim ionic liquidTutorial: A room-temperature ionic liquid - AmberIn this tutorial, we will be generating an ionic liquid mixture of 1-Butyl-3- methylimidazolium tetrafluoroborate ([ bmim ][BF4]) and Acetonitrile (CH3CN) to replicate ...
     24  -16 2014 sep 11tutorial9Amber tutorial - Protein Ligand binding free energiesSmall molecule binding to T4-lysozyme L99A. Overview. In this tutorial, free energy calculations will be used to calculate the relative binding free energy of two ...
     24  -3 2014 aug 14molecular modeling softwareAmber is a package of programs for molecular dynamics simulations of proteins and nucleic acids. ... pbsa, Performs numerical solutions to Poisson-Boltzmann models ... the release (on April 15, 2014) of version 14 of the Amber software suite.
     25  +14 2014 sep 01create esp fileGenerate topology file for 4-hydroxyl-Proline - AmberGenerate two gaussian input files: alpha and beta using the following ... Extract ESP files from gaussian output files ( alpha and beta ) and merge them together ...
     26  +75 2014 sep 30build your own v string gaffAMBER 14 manualD.A. Case, V . Babin, J.T. Berryman, R.M. Betz, Q. Cai, D.S. Cerutti, T.E.
     26  +3 2014 sep 26www ntpr ruRe: [AMBER] nothing is written to .mdcrd file from Carlos Simmerling it might be worth a test run with shorter nstlim and ntpr =1 so you can see ... 2010 at 10:15 AM, Andrew Voronkov <drugdesign.yandex. ru >wrote:
     27  +21 2014 sep 30use nvidia teslaSupport for NVIDIA GPU acceleration of AMBER PMEMD Calculations by Ross ... GPU is used , for example you have a Tesla C2050 (3GB) and a Tesla C2070 ...
     27  +3 2014 sep 10rdisrdis - AmberRdis takes the input values in the range {min_val ... max_val} and counts the frequency of occurrence of values in each of n_points intervals (bins) in the range .
     27  -13 2014 aug 29yahoo amber antonAmber 12 Reference ManualWhen citing Amber 12 in the literature, the following citation should be used:
     27  -13 2014 jul 31c force tutorialAn Amber Lipid Force Field TutorialAn Amber Lipid Force Field Tutorial : Lipid14 Edition. Benjamin D. Madej, Ross C . Walker Updated May 27, 2014. Lipid_Bilayer ...
     28  +18 2014 oct 04tutorial exchange linkAmber TutorialsA set of tutorials for learning how to use the AMBER molecular dynamics software . ... This tutorial covers how to setup, run and postprocess replica exchange  ...
     28  +9 2014 sep 25field force softwareAmber is a package of programs for molecular dynamics simulations of proteins ... "Amber" refers to two things: a set of molecular mechanical force fields for the ...
     28  +4 2014 aug 12act software tutorialsThe aim of this tutorial is to act as a brief introduction to running classical molecular dynamics simulations using the AMBER software . In this tutorial we will  ...
     29  +72 2014 sep 23refrain from illusionsRe: [AMBER] R.E.D. : Gaussian Error - amber mailing list archiveREFRAIN FROM ILLUSIONS , INSIST ON WORK AND NOT WORDS, PATIENTLY SEEK DIVINE AND SCIENTIFIC TRUTH. LAST WORDS OF ...
     30  ~ 2014 sep 30dating script expensiveAmberTools13 Reference ManualMMPBSA.py is a python script that automates energy analysis of ... also an older perl script , called mm_pbsa.pl, that is a part of Amber.).
     30  ~ 2014 sep 17dap dnaGenerate topology file for nucleotide with the phosphate group Generate a gaussian input file: dna .gau from a mol2 file dna .mol2 ... and a mainchain defination file mainchain. dna to generate prep input file ( DAP , DCP, DGP, ...
     30  +71 2014 sep 12stds k7dual K7 (was Re: Linux-cluster performance) from Tru Huynh on dual K7 (was Re: Linux-cluster performance) ... std 0.0 0.0 0.0 0.0 0.0 0.0 0.0 min 0.0 89.9 0.7 0.4 0.0 ... std 0.1 1.0 0.1 0.0 0.0 0.0 0.0 min 0.9 ...
     30  ~ 2014 aug 24mtv api deprecatedAmberTools12 Reference ManualInformation on some older (now obsolete ) force fields in given in Appendix B.
     31  +28 2014 aug 28adrian merz post-it roomD.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz , Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods.
     32  -6 2014 aug 15dynamic simulation modelling softwareAmber is a package of programs for molecular dynamics simulations of proteins and nucleic acids. ... Assisted Model Building with Energy Refinement. "Amber" ...
     33  -9 2014 aug 26dat file formatFile formats - AmberAMBER file formats ..... E.g. if you specify STDA in parm.in for the "regular" parm. dat file , this is the convention that will be used when reading frcmod. End with a ...
     34  -3 2014 oct 1220 unisiAMBER: PCA from venditti2. unisi .it on 2006-04-06 (Amber Archive From : <venditti2. unisi .it> Date : Thu, 06 Apr 2006 22:27: 20 +0200 (CEST). Dear all, there is a way to filter a trajectoy to diplay only the motion ...
     34  +67 2014 sep 27filip malýRe: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? from On Wed, 3/30/11, Marek Maly <marek. maly .ujep.cz> wrote: > From: Marek ... Filip just for the curiosity, which linux distribution do > you use ? >
     34  ~ 2014 sep 25shape model of the nucAmber Basic Tutorials - Tutorial B1 - Section 2This should produce a nuc .pdb file, which is the model structure of our DNA duplex. ..... A more efficient shape to use, in terms of reducing the problem of solute ...
     34  +11 2014 sep 25aol wikipwediaRe: [AMBER] Calculating Amber Force fields from Wikipedia from From : Whimsica. aol .com <whimsica. aol .com> Date : Mon, 15 Mar 2010 08:32:57 -0700. The equation on wikipedia has electostatics torsions ...
     34  ~ 2014 sep 25r atp[AMBER] ATP parameters: tleap error - amber mailing list archiveCreating new UNIT for residue: ATP sequence: 1279. Created a new atom named: PG within residue: . R < ATP 1279> Created a new atom ...
     34  -6 2014 sep 22univ reimsRe: AMBER: TI, mutation from eric.henon. univ - reims .fr on 2006-08 From : <eric.henon. univ - reims .fr> Date : Tue, 29 Aug 2006 08:43:04 +0000. Thank you to Pradipta and Carlos for their response. E. Henon
     34  ~ 2014 sep 02miyoto air condition manualtory, and is described in Chapter 2 of the AmberTools manual .
     35  ~ 2014 sep 12unlimit robertRe: [AMBER-Developers] release plans from Robert Duke on 2010 From : Robert Duke <rduke.email.unc.edu> Date : Mon, 19 Apr 2010 16:42:21 - 0400. Well, I would say that not being to unlimit the stack size to ...
     35  +15 2014 aug 28pgi suite opensourceRe: [AMBER] compilation of amber12 on cray system from Jorgen PGF90-F-0002-Unable to open source input file: emap. ... PGF90/x86-64 Linux 12.4-0: compilation aborted ... Obtaining the PGI suite version:
     36  -4 2014 jul 29credit agreement licenceamber 12 software license agreementIMPORTANT: This Amber license Agreement is a legal agreement between you, the end ... When you have signed this license agreement and sent credit card ...
     38  +10 2014 sep 22dalong j typeantechamber packageAm1bcc reads in an ac file to assign atom types and bond types according to
     39  +24 2014 sep 30run on sunRunning Amber on Sun OSRunning Amber on Sun OS. This page is outdated (circa 2005). If you are an Amber user planning to run on SunOS then contact Scott Brozell via the AMBER  ...
     39  +33 2014 sep 23replica ch3Poly-Proline with AMBER 11.well) replica -exchange[1] technique. .... the PMF for the :1@ CH3 == :1@C == :2@ N == :2@CA dihedral of the Ace − (Pro)5 − NHe is close to.
     39  +62 2014 aug 03mailto con subjectRe: [AMBER] Memory test con GTX 470 - amber mailing list archiveFrom: Scott Le Grand [ mailto :SLeGrand.nvidia.com] Sent: Friday, September 10, 2010 1:35 PM To: AMBER Mailing List Subject : Re: [AMBER] ...
     40  +19 2014 sep 14vz icoAMBER File SpecificationsThe index is calculated as follows: index = ICO (NTYPES*(IAC(i)-1)+IAC(j)) If index is positive, this is an index into the 6-12 parameter arrays (CN1 and CN2) ...
     40  ~ 2014 aug 22best dynamic modeling softwareAmber is a package of programs for molecular dynamics simulations of proteins and nucleic acids. ... in a variety of simulation programs ); and a package of molecular simulation ... A good general overview of the Amber codes can be found in:.
     40  +61 2014 jul 31link exchange tutorial
     42  -21 2014 sep 10nvidia pci root id fixamber 12 nvidia gpu acceleration support
     42  +13 2014 sep 09nvidia cudaNVIDIA CUDA Implementation: Scott Le Grand (NVIDIA) Ross C. Walker (SDSC)* . *Corresponding author. Further information relating to the specifics of the ...
     42  ~ 2014 sep 08library filesOFF Library files - AmberOFF file format specification (written by Jason Swails, 2/20/2011): This document describes the format of Amber OFF library files . You may look at any of the ...
     43  +58 2014 sep 23pymakeRe: [AMBER] MMPBSA. py -make -mdins does not work with nmode Re: [AMBER] MMPBSA. py -make -mdins does not work with nmode. This message : [ Message body ] [ More options (top, bottom) ]; Related ...
     43  -11 2014 sep 20amalloccompile_errors_for_parallelused for linking /usr/lib64/libc. a(malloc .o)(.text+0x1e10): In function ` __libc_free': /usr/src/packages/BUILD/glibc-2.3/malloc/malloc.c:3360: multiple definition of ...
     44  ~ 2014 sep 11the starlight desktopRe: [AMBER] charmmlipid2amber.py from James Starlight on 2014 e.g trying own. starlight ~/ Desktop /Amber/tutorials/membrane $ sh vmd_box_dims .sh -i xz222.pdb -s water : not founds.sh: 2: vmd_box_dims.sh:
     45  -2 2014 sep 25select nvidia card for cuda
     45  ~ 2014 aug 16deal cu dor acordThe cifparse routines to deal with mmCIF formatted files were written by John
     46  -8 2014 sep 26benchmarks
     46  -12 2014 jul 20attn on packageA simple introduction to antechamber package . ... Be careful to those problem parameters marked by " ATTN , need revision". Usage Usage: parmchk -i input -o  ...
     47  +19 2014 sep 30types of forceGAFF - AmberCompared to traditional AMBER force field, atom types in GAFF are more general and cover most of the organic chemical space.Table I lists the basic (a) and ...
     48  -10 2014 aug 31atom in a boxLEaP - AmberSuperimposing a box of water on the solute & box and then subtracting overlapping waters leads to ... Total bounding box for atom centers: 16.686 9.719 8.133
     48  ~ 2014 aug 20english tutor advancedThe tutorials are divided into basic, advanced , and analysis-specific. ... TUTORIAL B3: Case Study - Folding TRP Cage ( Advanced analysis and clustering).
     49  +37 2014 sep 22tutorial 9With the release of AMBER 9 comes the ability to do very fast advanced coupled potential QM/MM driven minimisation and MD. This tutorial will show how to set ...
     49  +6 2014 aug 22name change doc prepAMBER Prep File SpecificationNOTE: Leap replaces Prep , Link, Edit and Parm with a much simpler, single .... access file containing the standard residues and a directory of their names . ... ' CHANGE ' It is input as cartesian coordinates or part cartesian and part internal.
     50  -12 2014 aug 22mailing list archiveAMBER MAILING LIST ARCHIVEThis is the Archive of the Amber Molecular Dynamics Software Mailing List . This contains many messages from amber users and developers discussing the ...
     51  -29 2014 sep 20qm error 11Re: [AMBER] PM6-DH+ QM /MM-GBSA - amber mailing list archiveOn Tue, 2014-03- 11 at 10:38 +0100, Kanin Wichapong wrote: > Dear AMBER ... However, when I tried these methods, I got an error as: > >
     51  -15 2014 sep 19soft core freeAMBER: For help: Thermodynamic Integration of solvation free I am trying to calculate the solvation free energy of benzene using newly developed soft - core potential, just as the Amber tutorial A9.
     52  -8 2014 sep 30simulated annealingSimulated Annealing - AmberSimulated Annealing and Equilibration. We will now run 100ps of MD at 300K with a much bigger spring constant. This will allow the structures to explore the ...
     52  -27 2014 sep 01dielectric constant of waterDielectric constant with water - AmberWhat dielectric constant with water ? I would very much appreciate receiving AMBER users' opinions on the best way to set the dielectric multiplicative constant ...
     52  +38 2014 aug 14sasa re sasaRe : [AMBER] residue-wise SASA calculation in CPPTRAJ from From : Jason Swails <jason.swails.gmail.com> Date : Tue, 26 Mar 2013 07:54:31 -0400. On Tue, Mar 26, 2013 at 6:08 AM, aneesh cna ...
     52  -16 2014 aug 11create tutorial softwareIn this tutorial we will create a initial structure for a 10-mer of DNA and then we .... In this tutorial we will learn how to use the AMBER software coupled with the ...
     53  -19 2014 oct 01windows cygwinSupport of Amber and AmberTools under Microsoft Windows . ... General remarks | Installation on Windows using Cygwin | | Installation of the native Windows  ...
     53  +48 2014 sep 26courtney stantonProblem with LES topology file from Courtney Stanton on 2003-06 From : Courtney Stanton <cstanton78.hotmail.com> Date : Tue, 17 Jun 2003 15: 28:10 -0700. Hello all, I am trying to use the undocumented ...
     53  -20 2014 sep 19number of framesRe: [AMBER] Count number of frames in any trajectory file from The number of frames is stored in the netcdf file, but not formatted. ASCII trajectories. Ptraj and cpptraj get the number of frames directly from ...
     53  ~ 2014 sep 15بروتين نو 99 , 3878-3888 (2013). ... The sander program is now a part of AmberTools. ... Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ...
     55  +7 2014 sep 25sighn tologyThe following section provides a good overview of the general topology file ..... FORMAT(A2,2X,F10.2x,f10.2) KNDSYM The unique atom symbol used in the ...
     55  +20 2014 sep 13ncsu gmailRe: [AMBER] ncsu input - amber mailing list archiveFrom : Daniel Sindhikara <sindhikara. gmail .com> Date : Fri, 22 Oct 2010 21:25: 06 +0900. I wonder, did you get an ncsu -smd.log file come out?
     57  -4 2014 aug 28energy simulation softwareAmber is a package of programs for molecular dynamics simulations of proteins and ... Assisted Model Building with Energy Refinement .... We are pleased to announce the release (on April 15, 2014) of version 14 of the Amber software suite.
     57  -27 2014 aug 17amber mac bookRe: [ AMBER ] Compiling Ambertools 1.4 on MacBook I've seen/used both on a Mac , with equivalent results... I don't know if LD is strictly for static libraries (in which case, don't use it for Macs ).
     58  -7 2014 sep 18numionbugfix.17 - Amber... + + double get_minvdwr( const vector<molecule_t>& ionlst ) + { + double minr = 1000.0; + int numion = ionlst.size(); + for( int i=0; i < numion ; ...
     58  ~ 2014 sep 09root geneyRestraints can also be defined in terms of the root -mean-square ..... the root - mean-square of the Cartesian elements of the gradient is less than ...
     58  +27 2014 aug 22macintosh picasso users manualAmber 10 Users ' ManualAmber is the collective name for a suite of programs that allow users to carry out molecular
     59  +42 2014 sep 12unbutu 11Installing Amber on LinuxAll of Amber will compile and run on Ubuntu Linux platforms (and variants like ... If you aren't ready to do this, then just configure AMBER with the - noX11 option.
     59  ~ 2014 aug 19english tutor advnace
     59  ~ 2014 aug 14template for da journalD.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, III, S. DeBolt,
     60  -2 2014 sep 06forcefieldA successful force field in drug design should work well both for the biological molecules and the organic molecules. AMBER force field has high reputation for  ...
     60  -14 2014 aug 10snow leopard gcc[AMBER] Compiling Amber10 on Mac Snow Leopard with gcc /gfortrancompiling Amber10 on Mac running Snow Leopard (10.6) using gcc /gfortran, but am running into an undefined symbols error when compiling ...
     61  -5 2014 sep 25r gtp[AMBER] How to make parameter files of GTP from PDB file. (B from The error message, Created a new atom named: O2* within residue: . R < gtp 1> Created a new atom named: HO*2 within residue: . R < gtp 1>
     61  -1 2014 sep 10pdb mapWhen LEaP loads a PDB file it tries to match the residue name in the PDB ... Use a PDB atom map , in LEaP (see "help addpdbatommap" and the default leaprc).
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