hole¶
Description¶
It can be used to calculate radius of protein channel/cavity for GROMACS MD trajectory. It uses HOLE program to calculate radius of cavity/channel and dumps the output to a text file as a function of time. It also extract channel’s outlining residues and dumps to same output file. This output file can be further read to perform final statistical operations and plotting.
- Please cite the original publication of hole:
- O.S. Smart, J.M. Goodfellow and B.A. Wallace (1993). The Pore Dimensions of Gramicidin A. Biophysical Journal 65:2455-2460.
Command summary¶
gmx_clusterByFeatures hole [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
[-n [<.ndx>]] [-o [<.dat>]] [-pdb [<.pdb>]] [-b <time>]
[-e <time>] [-dt <time>] [-tu <enum>] [-[no]fit]
[-endrad <real>] [-sample <real>] [-cvect <vector>]
[-cpoint <vector>] [-catmid <int>] [-rad <enum>]
| Option | Default | File type |
|---|---|---|
| -f [<.xtc/.trr/…>] | traj.xtc | Trajectory: xtc trr cpt gro g96 pdb tng |
| -s [<.tpr/.gro/…>] | topol.tpr | Structure+mass(db): tpr gro g96 pdb brk ent |
| -n [<.ndx>] | index.ndx | Index file |
| Option | Default | File type |
|---|---|---|
| -o [<.dat>] | radius.dat | Generic data file containing matrix |
| -pdb [<.pdb>] | sphpdb.pdb | PDB file for scpheres along the radius |
| Option | Default | Description |
|---|---|---|
-b <real> |
0 | First frame (ps) to read from trajectory |
-e <real> |
0 | Last frame (ps) to read from trajectory |
-dt <real> |
0 | Only use frame when t MOD dt = first time (ps) |
-tu <keyword> |
0 | Unit for time values: fs, ps, ns, us, ms, s |
| -[no]fit | Enable | Enable fitting and superimposition of the atoms groups. |
| -endrad <real> | 5 | Radius value (A) after which calculation is stopped. |
| -sample <real> | 0.5 | The distance between the planes for the sphere centers. |
| -cvect <vector> | 0 0 1 | Vector along the channel |
| -cpoint <vector> | 999 999 999 | Coordinate within a channel as seed for channel/cavity. |
| -catmid <int> | -1 | Serial number of atom, whoose coordinate acts as seed for channel/cavity. |
| -rad <keyword> | bondi | Radius type for atoms. |
Options to specify input files¶
-f traj.xtc¶
Input trajectory file of xtc trr cpt gro g96 pdb or
tng format.
-s topol.tpr¶
An input structure file of tpr gro g96 or pdb format.
-n index.ndx¶
Two index groups from this file will be prompted for selection. Otherwise, default index groups will be prompted for selection.
Minimum-distance matrix will be calculated between the two selected atom-groups.
Options to specify output files¶
-o radius.dat¶
Output file containing channel/cavity axis, radius and outlining residues as a function of time.
-pdb sphpdb.pdb¶
Output PDB file containing coordinates of sphere inside the channel/Cavity. Radius of these sphere is channel/cavity radius. This file can be used to visualize whether obtained radii are from inside the intended channel/cavity.
Other options¶
-fit/-nofit¶
Weather to superimpose structures on reference structure using least-square fitting.
-endrad 5¶
Radius (A) above which the HOLE program regards a result as an indication that the end of the pore has been reached
-sample 0.5¶
The distance (A) between the planes for the sphere centers
-cvect 0 0 1¶
This specified a vector which lies in the direction of the channel/cavity.
-cpoint 999 999 999¶
A point which lies within the channel. If not given, center of mass will be used. This point will be used a seed to start calcualtion for channel/cavity radius.
Note
Due to this option, superimposition of structures on reference structure is necessary.
Note
Conformations changtes during the simulations, therefore, this
coordinate may not be inside the cavity. To dynamically select seed coordinate,
use -catmid option.
-catmid -1¶
Serial number of atom, which lies within the channel and acts as a seed for channel/cavity. If not given, center of mass will be used. It can be used to assign seed-coordinate dynamically.
-rad bondi¶
Radius of atoms considered during channel/cavity calculation.
- Accepted categories of radii are:
bondi- For all-atom force-fields, this category can be used.amberuni- For united-atom force-fields, this category can be used.downscaledhardcoresimple- For united-atom force-fields, this category can be used.xplor
These radii are taken from original HOLE implementation. For values of these radii, please follow this link.