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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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> 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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No Amber parameter file needs to be generated prior to using this utility, but if an appropriate parameter/topology file is available it may be given with -partop. As in <docmark>minAmber.pl</docmarl> the location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC.

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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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From: Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de> Date: Sat, 28 Aug 2010 10:32:23 +0200 Dear all, we have problems reading trajectories that were generated with sander from Amber8 using the binary format (IOUTFM=1). We tried ptraj from

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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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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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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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We no longer need the amber target in the shards.yml for new projects since amber will exist on the docker image already. The image will match the release version. This allows for older versions of amber to continue to work without breaking changes. The official amber docker image can be used on all platforms that support docker.

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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.

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> The binary formats in AMBER are old; they are not transferable among > different hardware (for example SGI vs. Linux) meaning that in general you > need to re-read them on the platform that produced them to be safe using

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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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