Tools and information for AMBER and CPPTRAJ examples
Updated: December 8, 2022
Reorienting small molecules to fit the orientation of another molecule You want to screen a collection of small molecules into a receptor but need to re-orient them to match a starting structure. In this recipe we will use… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General, General Concepts, Topology File Commands, Tutorials
Updated: March 28, 2019
Parameter and reference files may be ’tagged’ (i.e. given a nickname). These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More
Posted: February 20, 2019
Ranges instead of atom masks. For several commands some arguments are ranges (e.g. ’trajout onlyframes <range>’, ’nastruct resrange<range>’, ’rmsd perres range <range>’); THESE ARE NOT ATOM MASKS. They are simple number ranges using ’-’ to specify a range… Read More
Updated: January 26, 2024
The mask syntax is similar to PTRAJ. Note that the characters ’:’, ’@’, and ’*’ are reserved for masks and should not be used in output file or data set names. All masks are case-sensitive. Either names or… Read More
Updated: February 20, 2019
Cpptraj uses the AKMA system of units. The exception is time, which is typically expressed in ps (except where noted). Variable Unit Length Angstrom Energy kcal/mol Mass AMU Charge electron Time ps (typically) Force kcal/mol*Angstrom
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