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Dear Amber users, I would like to implement my own analysis program and one of the functions I need is to be able to read in binary trajectories (AMBER or CHARMM) Does anyone know how I can go about doing this? That is, what is the file format ..etc. Much Thanks! Grace ----- The AMBER Mail Reflector To post, send mail to amber.scripps.edu

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AMBER ADVANCED WORKSHOP. TUTORIAL 4. AMBER Refinement of a DNA Duplex [created by Vickie Tsui; updated by Rhonda Torres. ] There is no single recipe to the "best NMR refinement." The route chosen for refinement of a particular system, in the end, is a mixture of common sense, trial and error, and personal taste.

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AMBER Archive (2007) - AMBER: Binary file curiosities

As in minAmber.pl the location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least AMBERHOME should be set accordingly. Otherwise an attempt is made to locate the Amber binary from the search path and deduce the data directory from the binary location.

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> In case other AMBER users want do this this with > fortan as well, I am including a rather pointless pseudo code that should > work for reading the binpos format using a fortran compiler that supports > the "binary" form option. Thanks. I've been reluctant to use this, since (as far as I can tell, e.g.

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> "features" of AMBER. For instance, from what I can tell from mdwrit.f, if > you choose the option NTRX=1 in sander you get an unformatted file that > looks exactly like the formatted mdcrd file. However, I do not see the > option to write these types of files from ptraj, only binpos binary files > are available (from my inspection of

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Hi Amber folks, I have been playing with reading the various binary AMBER trajectory data types lately, and I noticed a few things that strike me as puzzling "features" of AMBER. For instance, from what I can tell from mdwrit.f, if you choose the option NTRX=1 in sander you get an unformatted file that looks exactly like the formatted mdcrd file.

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When I add the "aniso" option ("solvateoct model TIP3PBOX 10 10 10 10 aniso"), I get the following, which does not give me an isotropic truncated octahedron even though I've specified equal x, y, and z dimensions: Scaling up box by a factor of 1.421552 to meet diagonal cut criterion Solute vdw bounding box: 23.884 20.817 22.394

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AMBER Trajectory NetCDF Convention. Beginning with AMBER 9, a binary file format for trajectory data based on NetCDF is supported by sander, pmemd and ptraj. This format is supported by VMD beginning with version 1.8.4. The AMBER Trajectory NetCDF Convention, describes the

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A note on force fields: A number of different force fields are supplied with AMBER. In AMBER v5.0 and v6.0 the default field was the Cornell et al. (1995) or parm94.dat force field (referred to as FF94 in AMBER v8.0 and later). In AMBER v10.0 and 11 the force field recommended for the simulation of proteins and nucleic acids in explicit solvent was either the FF99SB or the FF03 force field

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AMBER Archive (2007) - Re: AMBER: Binary file curiosities

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2019/04/18 · If you want to write out an Amber restart file, you need to either provide the recognized extension for the output trajectory filename (.rst7) or specify the 'restart' keyword to 'trajout', e.g.

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See AMBER documentation for netCDF format description. NetCDF binary trajectory files are supported by the AMBER modules sander, pmemd and ptraj. Compared to formatted trajectory files, the binary trajectory files are smaller, higher precision and significantly faster to read and write.