esander

Calculate energies using via SANDER; requires compilation with the SANDER API.

esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles] [<namelist vars> ...]

[<name>] Data set name.
[out <filename>] File to write results to.
[saveforces] If specified, save forces to frames. Requires writing frames in NetCDF format.
[parmname <file>] Name of temporary topology file (default: ’CpptrajEsander.parm7’).
[keepfiles] Keep temporary topology file after program execution.
[<namelist vars>] Namelist variables supported by the sander API in format ’var <value>’; see below.

Calculate energies for input frames using the sander API. It requires compilation with the SANDER API (sanderlib). This can be considered as a faster alternative to energy post-processing with sander (imin = 5). Currently the following sander namelist variables are supported: extidel, intdiel, rgbmax, saltcon, cut, dielc, igb, alpb, gbsa,
lj1264, ipb, inp, vdwmeth, ew_type, ntb, ntf, ntc. See the SANDER entry of the AMBER manuals for details. If ntb/cut/igb are not specified cpptraj will attempt to pick reasonable values based on the input system. The defaults for a non-periodic system are ntb=0, cut=9999.0, igb=1. The defaults for a periodic system are ntb=1, cut=8.0, igb=0. This currently requires writing a temporary Amber topology, the name of which can be set by parmname. If keepfiles is specified this temporary topology will not be deleted after execution.

For example, to calculate energies for a non-periodic system using igb=1 (the default) with GB surface area turned on (gbsa=1):

parm DPDP.parm7
trajin DPDP.nc
esander DPDP out Edpdp.dat gbsa 1