Tools and information for AMBER and CPPTRAJ examples
Updated: May 20, 2019
You want to compare the structural difference caused by the binding of 6 different ligands to the same protein receptor. First we need to create a reference structure that has no ligand that will serve to compare the… Read More
Updated: July 1, 2023
Write write [invert] [noxcol] [groupby <type>] [noheader] [square2d|nosquare2d] [nosparse|sparse [cut <cutoff>]] invert Normally, data is written out with X-values pertaining to frames (i.e. data over all trajectories is printed in columns). This command flips that behavior so that… Read More
Updated: July 1, 2023
For more information on Grace see http://plasma-gate.weizmann.ac.il/Grace/. Write [{invert|noinvert}] [{xydy|noxydy}] [<label set>] invert Normally, data is written out with X-values pertaining to frames (i.e. data over all trajectories is printed in columns). This command flips that behavior… Read More
Updated: July 1, 2023
For more information on these options it helps to look at the PM3D options in the Gnuplot manual (http://gnuplot.info/). Write [{nolabels | labels}] [usemap | pm3d | nopm3d] [title <title>] [jpeg] [noheader] [{xlabels|ylabels|zlabels} <labellist>] nolabels Do not… Read More
Updated: March 30, 2019
Note that multiple REM logs can be specified in a single readdata command. Read [nosearch] [dimfile <file>] [crdidx <crd indices>] [nosearch] If specified do not automatically search for MREMD dimension logs. [dimfile <file>] remd.dim file for processing MREMD… Read More
Updated: March 30, 2019
Note that multiple MDOUT files can be specified in a single readdata command.
Updated: March 30, 2019
Read [ibeg <firstmode>] [iend <lastmode>] ibeg <firstmode> Number of the first mode (or principal component) to read from evecs file. Default 1. iend <lastmode> Number of the last mode (or principal component) to read from evecs file. Default… Read More
Updated: December 8, 2023
This can be used to write out a representation of a vector data set which can then be visualized. See the vector command for more on generating vector data sets. [trajfmt <format>] [parmout <file>] [noorigin] trajfmt <format> Output… Read More
Updated: March 29, 2019
Write [bincenter] [gridwrap] [gridext] bincenter Center grid points on bin centers instead of corners. gridwrap Like ’bincenter’, but also wrap grid density. Useful when grid encompasses unit cell. gridext Like ’bincenter’, but also print extra layer of empty… Read More
Updated: March 29, 2019
Write [title <title>] [title <title>] Set CCP4 output title.
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