evalCovalent
Analyze coordinates for covalent (bond, angle, improper dihedral) violations.
Usage: evalCovalent [options] <coordinate files to analyze>
where option is one or more of:
-bondThresh <val> - bond length difference (in Angstrom) from
equilibrium above which a violation is
flagged [0.05]
-angleThresh <val> - bond angle difference (in degrees) from
equilibrium above which a violation is
flagged [2]
-imprThresh <val> - impropropoer dihedral difference (in degrees)
from equilibrium above which a violation is
flagged [2]
-selection <atom selection> - atoms to include in analysis selection
-psf <file name> - PSF file - required for nonstandard residues
-par <file name> - filename containing alternate parameters - may
be specified more than once.
-top <file name> - filename containing alternate topology. To
replace the topology for a system, specify
the system name as system:filename using a
colon as a separator.- may be specified more
than once.
-fixImpropers - If specified, set fixMethylImpropers and
fixProtonImpropers to True in
protocol.initCoords, else they are set to
False
-model <integer> - PDB model number to read [1]