Salt Bridges Plugin, Version 1.1
The Salt Bridges plugin searches for salt bridges formed in a protein throughout a trajectory. The search can be restricted to a selection and/or a frame range given by the user.
Criteria for the formation of a salt bridge
A salt bridge is considered to be formed if the distance between any of the oxygen atoms of acidic residues and the nitrogen atoms of basic residues are within the cut-off distance (default 3.2 Angstroms) in at least one frame. The default distance cut-off can be changed by the user. This plugin does not attempt to identify hydrogen bonds.
An additional distance cut-off between the centers of mass of the side-chain heavy atoms of oppositely charged residues can be specified.
Acidic and basic residues
The Salt Bridges plugin searches for salt bridges between amino acid residues identified with the VMD keywords acidic and basic, which are defined in the following way:
atomselect macro acidic "resname ASP GLU"
atomselect macro basic "resname ARG HIS LYS HSP"
In particular, this means that if all the histidine residues have resname HIS (often the case in original PDB files), all of them will be considered in the salt bridges calculation. On the other hand, if the histidine residues have resnames HSP, HSD, or HSE (as specified in the CHARMM force field), only the protonated histidines HSP will be considered in the calculation.
Update selections every frame
This plugin uses atom selections based on the atom selection given by the user. There are some cases in which the atom selection might change in time, such as:
- within or exwithin are used
- any one of the coordinates are used in a comparison (e.g., "x > 3"), or say "sqrt(sqr(x-50) + y*y + z*z) > 25)"
- the selection is based on atoms next to specific voxel values
- the "user" field is used in a selection (time varying)
If the selection used does not change in time, the option "update selections every frame" can safely be disabled, which will increase the efficiency of the calculation.
Output files
By default, a file is written for each salt bridge, containing the frame number and the distance between the center of mass of the oxygens in the acidic side chain and center of mass of the nitrogens in the basic side chain. Note that this distance is slightly different than the criteria used to identify salt bridges (see above).
Command-line interface
All the functionalities of the plugin are also available through the command line interface.
Usage: saltbr -sel <atom selection> <option1> <option2> ...
Options:
- -upsel <yes|no> (update atom selections every frame? default: yes)
- -frames <begin:end> or <begin:step:end> or all or now (default: all)
- -ondist <cutoff distance between oxygen and nitrogen atoms> (default: 3.2)
- -comdist <cutoff distance between centers of mass of side chains> (default: none)
- -writefiles <yes|no> (default: yes)
- -outdir <output directory> (default: current)
- -log <log filename> (default: none)
