Analyze coordinates for RepelPot nonbonded clashes.
Usage: analyzeRepel [options] <coordinate files to analyze>
where option is one or more of:
-bumpSel <val> - atoms to perform detailed analysis on
-bumpDist <val> - distance bound for -bumpSel analysis [3]
-repel <val> - Radius scale [default]
-threshold <val> - overlap above which a violation is flagged
[0.2]
-selection <atom selection> - atoms to include in Repel selection
-selPair <atom sel1> <atom sel2> - add a pair of selections to compute
interactions between
-psf <file name> - PSF file - required for nonstandard
residues
-par <file name> - filename containing extra nonbonded
parameters
-model <integer> - PDB model number to read [1]
-use14 - if specified, included 1-4 interactions in
computation