SPAM method for estimating relative free energies of waters in hydration shell around proteins.

spam <filename> [solv <solvname>] [reorder] [name <name>] [purewater] [cut <cut>] [info <infofile>] [summary <summary>] [site_size <size>] [sphere] [out <datafile>] [dgbulk <dgbulk>] [dhbulk <dhbulk>] [temperature <T>]

<filename> File with the peak locations present (XYZ- format)
<solvname> Name of the solvent residues
<cut> Non-bonded cutoff for energy evaluation
<dgbulk> SPAM free energy of the bulk solvent in kcal/mol; default is -30.3 kcal/mol (SPC/E water).
<dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol; default is -22.2 kcal/mol (SPC/E water).
<T> Temperature at which SPAM calculation was run.
<infofile> File with stats about which sites are occupied when.
<size> Size of the water site around each density peak.
[sphere] Treat each site like a sphere.
[purewater] The system is pure water—used to parametrize the bulk values.
[reorder] The solvent should be re-ordered so the same solvent molecule is always in the same site.
<summary> File with the summary of all SPAM results. If not specified, no SPAM energies will be calculated.
<datafile> Data file with all SPAM energies for each snapshot.

Perform profiling of bound water molecules via SPAM analysis. Briefly, this method identifies and estimates the free energy profiles of bound waters via calculation of the distribution of interaction energies between the water and it’s environment from explicit solvent MD trajectories. The interaction energies are calculated using a force and energy-shifted electrostatic term with a hard cutoff.

Prior to this command, the volmap command should be run with the peakfile keyword to generate the peaks file. If not using peaks from the volmap command, the peaks file should have one line per peak with format:

C <X> <Y> <Z> <Density>

Values of dgbulk and dhbulk for different water models can be calculated from pure water simulations with the purewater keyword.