Subsections
4.4 Output
FRED's primary outputs are hitlist(s) of top scoring molecules (FRED also outputs
several auxiliary files during the course of the run, see section
5.7 for a complete list of output files).
A hitlist will be maintained for each of the scoring functions
the user selected. If multiple scoring functions are selected
FRED will also maintain a consensus scoring hitlist using all the scoring
functions selected. If no scoring functions are selected by the user FRED will
default to using Chemgauss3 scoring.
Each hitlist can be output to up to 4 files, each with a different representation
of the hitlist. Those are:
Structure- This file contains the conformer and location of the top scoring
pose of each ligand sorted by score. The format is one of the standard
molecular file formats supported by FRED (see section B), which
can be selected using the -oformat flag. The name of the file will be
<scoring function>_docked.<file ext>
Where <scoring function> is the name of the scoring function and
<file ext> corresponds to the file extension corresponding to the file
format.
For file formats that support storing scoring information (.oeb and .sdf at
the time of this writing) the total score and score components are written
into the structure file.
Alternate Structure- This file contains the structure of the top
scoring pose and alternate poses for each ligand. The top scoring ligand's pose
and its alternates are listed first, followed by the second best scoring ligand's
top pose and its alternates and so on. The format is one of the standard molecular
formats supported by FRED (see section B), which can be
selected using the -oformat flag. The name of the file will be
<scoring function>_alt_docked.<file ext>
Where <scoring function> is the name of the scoring function and
<file ext> corresponds to the file extension corresponding to the file
format.
For file formats that support storing scoring information (.oeb and .sdf at
the time of this writing) the total score and score components are written
into the structure file.
Score- This text file lists the name, total score, score components
and SMILES representation of each ligands top ranks pose. The name of the file
will be
<scoring function>_scores.txt
Where <scoring function> is the name of the scoring function.
Alternate Score
This text lists the name, total score, score components and SMILES
representation of each ligand top rank pose and alternates.
The name of the file will be
<scoring function>_alt_scores.txt
Where <scoring function> is the name of the scoring function.
Note that the names of these files can be modified by
adding a prefix specified with the -prefix flag.
4.4.2 Undocked molecules
Not every molecule that FRED reads can be docked and scored. Molecules that
FRED cannot dock have no score or docked structure and thus are not inserted
into the output hitlists described in the preceding section. Instead they
are outputted to a smiles to a file named
undocked_code<X>.smi
Where <X> is an integer return code describing why the molecules in that
file failed to dock. The meaning of each return code is as follows.
1 : Not Initialized- FRED failed to initialize the exhaustive
search properly.
2 : Empty Ligand- The molecule is empty (i.e., has no atoms).
3 : Empty Protein- The protein molecule is empty (i.e., has no atoms).
4 : Typing Error- FRED could not properly type the atoms of the molecule.
5 : Grid Setup Error- FRED could not create the grids it needs for the
exhaustive search, generally this is due to a lack of memory.
6 : Coordinate Error- There was an error reading one or more of the
atom coordinates, or generating extended coordinates for the molecule
(i.e., "lone pair" and "polar hydrogen" positions for the Chemgauss scoring
functions).
7 : No Constraint Match- The molecule does not have the required
functionality to match one or more constraints. (e.g., a constraint
requires that a donor on the ligand interact with the protein, but the ligand
does not have any donors).
8 : No Valid Poses- During the exhaustive search after filtering
the initial pose ensemble using the inner/outer contours and any specified
constraints there were no poses.
9 : Aborted- The user aborted the docking process. This can happen
in the fred_receptor GUI's trial docking mode, but not with the FRED
command line program.
10 : Fredcore Error- This return code is not used.
11 : Outside Grid- This return code is not used.
12 : Optimization Error- Solid body refinement of the molecule
failed.
13 : Consensus Error- The consensus structure stage of docking failed.
14 : Refinement Error- FRED was unable to refine the molecule, this
error generally because the molecule has atoms not recognized by the Merck
Molecular Mechanics Force Field.
15 : Invalid Refinement- Refinement of the molecule caused it to
move outside the site box defining the active site, or caused it to violate
user specified constraints.
16 : Missing MASC Data- A masc variant scoring function was used,
but the molecule did not have the required MASC data.
17 : Invalid Score- An error occurred during scoring that resulted
in an invalid floating point value for one of the scores.
18 : Lost- This error indicates that the molecules was never
returned from the slave during a multiprocessor run. This error generally
occurs when one of the nodes used in a multiprocessor run goes down or
loses contact with the network.
Having undocked molecules does necessarily indicate an error has occurred.
For example, the undocked molecules with return code 8, No Valid Poses,
will commonly occur when docking a typical ligand database to a small
internal active site because FRED recognizes larger molecules simply
cannot fit within the active site.
