Functions
	readXYZUser fn

	setBondsFromTpr fn

	writePQR sel filename

	writePlumed sel filename

	writePlumedRef sel filename

	writePDBTER sel fname

	writeNullVelFile as fname

	getFasta osel

Detailed Description

Function Documentation

◆ getFasta()

getFasta			osel

Returns the 1-letter sequence of a selection (looking at CA only)

◆ readXYZUser()

readXYZUser			fn

Load the optional data columns of a XYZ file in the "user" properties. Coordinates are ignored. Topology must be correct.

◆ setBondsFromTpr()

setBondsFromTpr			fn

Read bonds connectivities stored in a GROMACS's .tpr file and apply it to the current molecule. Unfortunately solvent bonds do not seem to show up (e.g tip3). The current connectivity is discarded. Requires "gmxdump" (of a sufficiently new version for your topology). Tested with gromacs-5.0. Not that different wrt. http://md.chem.rug.nl/cgmartini/index.php/rb

◆ writeNullVelFile()

writeNullVelFile			as fname

Write null velocity file corresponding to the current structure

◆ writePDBTER()

writePDBTER			sel fname

Write a PDB file containing TER cards to separate fragments. This is useful for software like ''tleap'' which requires them. ''$sel'' must be an atom-selection function (as returned by atomselect). For a fuller implementation, see also [[utilities/PdbTer]].

◆ writePlumed()

writePlumed			sel filename

Write a PDB file using charges and masses in the topology (required by PLUMED's "driver" utility)

◆ writePlumedRef()

writePlumedRef			sel filename

Write a PDB file to be used as a reference in PATH cvs. Assumes that occupancy and beta are set according to the align intentions.

◆ writePQR()

writePQR			sel filename

Write a crude PQR file using radiuses and masses in the topology (radii may not be appropriate for APBS calculations! use pdb2pqr instead!) Note that this preserves the CHAIN id. VMD PQR loader misparses the file.

Functions