Decomposition

&decomp namelist variables¶

idecomp (Default = None. Must be defined)

Energy decomposition scheme to use:

• 1: Per-residue decomp with 1-4 terms added to internal potential terms
• 2: Per-residue decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW potential terms
• 3: Pairwise decomp with 1-4 terms added to internal potential terms
• 4: Pairwise decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW potential terms

dec_verbose (Default = 0)

Set the level of output to print in the decomp_output file.

• 0: DELTA energy, total contribution only
• 1: DELTA energy, total, sidechain, and backbone contributions
• 2: Complex, Receptor, Ligand, and DELTA energies, total contribution only
• 3: Complex, Receptor, Ligand, and DELTA energies, total, sidechain, and backbone contributions

Note

If the values 0 or 2 are chosen, only the Total contributions are required, so only those will be printed to the mdout files to cut down on the size of the mdout files and the time required to parse them.

print_res (Default = "within 6")

Select residues whose information is going to be printed in the output file. The default selection should be sufficient in most cases, however we have added several additional notations

Selection schemes

By Distance (recommended)Amino acid selectionAll

Notation: [ within distance ]

within corresponds to the keyword and distance to the maximum distance criterion in Å necessary to select the residues from both the receptor and the ligand. In case the cutoff used is so small that the number of decomp residues to print < 2, the cutoff value will be increased by 0.1 until the number of decomp residues to print >= 2.

Example

print_res="within 6" Will print all residues within 6 Å between receptor and ligand including both.

Notation: [ CHAIN/(RESNUM or RESNUM-RESNUM) ]

Print residues individual or ranges. This notation also supports insertion codes, in which case you must define them individually

Example

print_res="A/1,3-10,15,100 B/25" This will print Chain A residues 1, 3 through 10, 15, and 100 along with chain B residue 25 from the complex topology file and the corresponding residues in either the ligand and/or receptor topology files.

Suppost that we can have the following sequence where chain A is the receptor and B is the ligand: A:LEU:5, A:GLY:6A, A:THR:6B, A:SER:6C A:ASP:6D, A:ILE:7 , B:25

Supported notationWrong notation

Ranges selection

print_res="A/5-7 B/25 Will print all mentioned residues because all residues with insertion code are contained in the range

Individual selection

print_res="A/5,6B,6C,7 B/25 Will print all mentioned residues except the residues 6A and 6D from chain A

print_res="A/5-6B,6D-7 Will end in error.

Notation: all

will print all residues. This option is often not recommended since most residues contribution is zero and it is just going to be a waste of time and computational resources.

Danger

Using idecomp=3 or 4 (pairwise) with a very large number of printed residues and a large number of frames can quickly create very, very large temporary mdout files. Large print selections also demand a large amount of memory to parse the mdout files and write decomposition output file (~500 MB for just 250 residues, since that’s 62500 pairs!) It is not unusual for the output file to take a significant amount of time to print if you have a lot of data. This is most applicable to pairwise decomp, since the amount of data scales as
O(N²).

Important

For GROMACS, we recommend using the reference structure (-cr) to ensure the perfect match between the selected residue in the defined structure or topology. For AMBER, NAMD and CHARMM we recommend check carefully the structure provided (-cs).

csv_format (Default = 1)

Print the decomposition output in a Comma-Separated-Values (CSV) file. CSV files open natively in most spreadsheets.

• 0: data to be written out in the standard ASCII format.
• 1: data to be written out in a CSV file, and standard error of the mean will be calculated and included for all data.