Tools and information for AMBER and CPPTRAJ examples
Updated: March 27, 2019
Retain only the specified number of solvent molecules closest to specified solute. closest <# to keep> <mask> [noimage] [first | oxygen] [center][closestout <filename>] [name <setname>] [outprefix <parmprefix>][parmout <file>] <# to keep> Number of solvent molecules to keep around… Read More
Updated: March 27, 2019
Report chirality around alpha carbons in amino acids (L, D). checkchirality [<name>] [<mask>] [out <filename>] [<name>] Data set name. [<mask>] Atoms to check. [out <filename>] File to write results to. DataSet Aspects: [L] Number of frames ’L’ for… Read More
Updated: March 27, 2019
Check for bad atomic overlaps or bond lengths. Can be used to skip corrupted frames. check [<mask>] [around <mask2>] [reportfile <report>] [noimage] [skipbadframes] [offset <offset>] [cut <cut>] [nobondcheck] [silent] [<mask>] Check structure of atoms in <mask> (all if not… Read More
Updated: June 12, 2020
Center specified coordinates to box center or onto reference structure. center [<mask>] [origin] [mass] [ reference | ref <name> | refindex <#> [<refmask>]] [<mask>] Center based on atoms in mask; default is all atoms. [origin] Center to origin… Read More
Updated: February 2, 2024
Set or overwrite box information for frames. box {[x <xval>] [y <yval>] [z <zval>] {[alpha <a>][beta <b>][gamma <g>][truncoct]} | nobox | auto [offset <offset> | getbox… Read More
Updated: February 26, 2020
Calculate the min/max coordinates for specified atoms. Can be used to create grid data sets. bounds [<mask>] [out <filename>] [dx <dx> [dy <dy>] [dz <dz>] name <gridname> [offset <bin offset>]] [<mask>] Mask of atoms to determine bounds of…. Read More
Updated: January 12, 2024
Calculate an average structure. Not to be confused with the avg command. average {crdset <set name> | <filename>} [<mask>] [start <start>] [stop <stop>] [offset <offset>] [Trajout Args] <filename> If specified, write averaged coordinates to <filename> (not compatible with… Read More
Updated: April 6, 2023
Automatically re-image coordinates. autoimage [<mask> | anchor <mask> [fixed <mask>][mobile <mask>]] [origin] [firstatom] [familiar | triclinic] [<mask> | anchor <mask>] Atoms to image… Read More
Updated: November 20, 2024
Attempt to create a map between atoms in molecules with different atom ordering. atommap <target> <reference> [mapout <filename>] [maponly] … Read More
Updated: January 26, 2024
Compute the atomic positional fluctuations. atomicfluct [<name>] [out <filename>] [<mask>] [byres [pdbres] | byatom | bymask] … Read More
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