Ludi



C       File Formats


Input Files--Ludi/Run background job

Table 8. Ludi/Run Input Files

Filenamea Linknameb Description
fragment_all.inp fort.4
fragment_link.inp
acd_subset.inp
<user_fragments_1>c   		Ludi fragment library (first of two files).  
fragment_all.pdb fort.9
fragment_link.pdb
acd_subset.struct
<user_fragments_2>c   		Ludi fragment library (second of two files).  
<run_name>.ludi_pdb fort.10   Protein pdb file (for receptor mode).  
<run_name>.ludi_pdb fort.3   Superimposed ligands pdb file (for active analog mode).  
<run_name>.ludi_inhib fort.7   Ligand file for link mode.  
<run_name>.ludi_inp   Ludi runtime parameters file.  
<run.name>.ludi.env   Library location file.  
aThe <run_name> is specified by the Run Name parameter in the Ludi/Run command.   bLinknames are runtime links to the files listed under Filename in this table. These links are removed when the Ludi/Run background job concludes successfully.   c<user_fragments_1> and <user_fragments_2> are fragment library files created by the user (e.g., using the Ludi/Add_Fragment command) or genfra.  

Ludi Fragment Library

Table 9. Ludi Library Files

standard libraries link libraries
fragment_all.inp <fort.4>   fragment_link.inp <fort.4>  
fragment_all.pdb <fort.9>   fragment_link.pdb <fort.9>  
acd_subset.inp <fort.4>   <user_fragments_1> <fort.4>  
acd_subset.struct <fort.9>   <user_fragments_2> <fort.9>  
<user_fragments_1> <fort.4>    
<user_fragments_2> <fort.9>    

Ludi fragment libraries are of two types: fragments used when Ludi is run in de novo mode (de novo library) and fragments used when Ludi is run in link mode (link library). There are two de novo libraries now available for Ludi. The fragment_all library contains a diverse set of fragments (approximately 1000 entries) and is released as part of Ludi. Ludi/ACD is a Ludi library available under separate license that contains all molecules in the MDL Available Chemicals Directory that are suitable for use with Ludi. The fragment_link library is the only link library available for use with Ludi and is released as part of Ludi. Customized de novo and link libraries may be created using the Ludi/Add_Fragment command in Insight II or the Unix-level command, genfra

A Ludi de novo or link library consists of two files, a structure file and a targets file. For each fragment in the Ludi library, there is an entry in the structure file that defines the element types and the coordinates of the atoms in the fragment. The structure entry is a multi-record entry; that is, it consists of more than one line. The first line of the structure entry specifies the fragment label and the number of atom records in the entry. The fragment label uniquely identifies the fragment within the library. The remaining lines in the structure entry define the fragment topology. The format of the topology section may either follow the format of Brookhaven Protein Data Bank (PDB) atom records or the format of MDL Mol files (including the header block, counts line, atom block and bond block). Connectivity is deduced from the atomic coordinates. The number of atom records may exceed the number of atoms in the fragment as some atoms may be listed twice for reasons that are explained below.

During a Ludi run up to six fragment atoms or groups of fragment atoms (the target sites) are fit onto a model of the receptor (the interaction sites). For example, when a receptor active site contains a hydrogen bond donor group, acceptor interaction sites are generated during a Ludi run. These interaction sites define the acceptable positions for a hydrogen bond acceptor that is participating in the hydrogen bond. Fragments with hydrogen bond acceptor target sites are then fit onto these interaction sites.

For each fragment in the Ludi library there is an entry in the targets file that specifies the type of each target site in the fragment. There are two acceptable formats for the targets file: a single record format and a multi-record format. Table 10 describes the format of a single-record targets entry. The first value in the single-record targets entry is the fragment label. The second value is no longer used because it has been replaced by a user-specified parameter. The remaining values specify the chemical types of the fragment's target sites. Each fragment has a minimum of two, and a maximum of six, target sites. Some of the chemical types refer to two-atom target sites and some to one-atom target sites. For example, hydrogen bond donating groups are two-atom target sites. Hydrophobic atoms are one-atom target sites. A description of the chemical types, including their classification as one- or two-atom targets, is given in Table 11.

Table 10. Format of the Targets File

Column(s) Description
1 - 4

 The library identifier.  
5 - 29

 No longer used. (Values may be present in older entries of the fragment libraries.)  
30, 40, 50, 60, 70

 Chemical types for fitting targets (see Table 11).  

Table 11. Target site chemical types used in the multi-record targets file

Chemical type index Description Example
-3   Hydrogen Acceptor   Alcohol Oxygen  
-1   Nonpolar Hydrogen   Methyl Hydrogen  
0   Undefined    
1   Hydrophobic Aliphatic   sp3 Carbon  
2   Hydrophobic Aromatic   sp2 Carbon  
3   Hydrogen Acceptor   Carbonyl Oxygen  
4   Acceptor Antecedent   Carbonyl Carbon  
5   Polar Hydrogen   Peptide Hydrogen  
6   Hydrogen Donor   Peptide Nitrogen  
7   Link Antecedent    
8   Link Atom    
9   Hydrogen Acceptor   Halogen  
10   Hydrogen Acceptor   Pyramidal Nitrogen  
11   Hydrogen Acceptor   Sulfone Oxygen  
12   Hydrogen Acceptor   Sulfoxide Oxygen  
13   Hydrogen Acceptor   Sulfate Oxygen  
14   Hydrogen Acceptor   Phosphate Oxygen  
15   Hydrophobic Aromatic   sp Carbon  
16   Hydrogen Acceptor   sp3 Phosphorous  

Each entry in the single-record targets file corresponds to an entry in the structure file. Each value in the targets entry that specifies the chemical type of a target site corresponds to one or two records in the structure entry. The first chemical type value in the targets file corresponds to the first or the first two atom records in the structure entry. If the chemical type specifies a one-atom target, the correspondence is to the first atom record of the structure entry. If the chemical type specifies a two-atom target, the correspondence is to the first two atom records of the structure entry.

Figures 4 and 9 reproduce link library entries for ribose with a single-record targets file format. Figure 4 is in PDB format and Figure 5 is in MDL mol format. For each entry, the first target atom is a type 7, a link group. A link group is a two-atom target and so the correspondence is to the atom records for C1 and C2. The second chemical type is -3, a hydrogen bond accepting atom. A hydrogen bond accepting atom is a one-atom target and so the correspondence is to the atom record for O4. The third chemical type is 5, a hydrogen bond donating group. The hydrogen bond donating group is a two-atom target and the correspondence is to the atom records for H6 and O6. Similarly, the fourth and fifth chemical types are 5, hydrogen bond donating groups, and the correspondence is to the atom records for H8 and O8 and to H12 and 012, respectively.

Figure 4 . Annotated Link Library Entry for Ribose, MDL Mol format.

The last field of the first line of the structure file entry identifies the format of the library, either MOL_FORMAT or PDB_FORMAT. If the format tag is missing the library is assumed to be in PDB format.

The first field of the first line of the structure entries for both PDB format and MDL mol format libraries gives a 4 character library identifier. This identifier must be unique across all entries in the library. The first three characters are chosen by the user (Ludi/Add_Fragment Label parameter) and the last character is appended by the Ludi/Add_Fragment background job.

The second field of the first line in a PDB format entry and the first field of the fifth line in a MDL mol format entry gives the number of ATOM records in the entry. The number may exceed the number of atoms in the fragment. This occurs when an atom is a member of more than one target site. As an example, consider the N in an NH2 group. Either of the two hydrogens can be donated in a hydrogen bond so there are two hydrogen bond donating target sites and each will contain an atom record for the N. These "duplicate" atoms are removed after the fragment is fit to the interaction sites.

The second and fourth lines of the MDL mol format entry give the molecule name and a comment that is entered at the Ludi/Add_Fragment parameter block.

The second field of the fifth line of the MDL mol format entry specifies how many BOND records follow the ATOM records. The first two numbers in a BOND record specify the bonded atoms and the third number specifies the bond order. The atom specification refers to the number of the ATOM record, e.g., 1 indicates the first atom listed in the ATOM records.

The "M END" and "$$$$" lines indicate the end of the MDL mol format entry. 


 






Figure 5
.  Format for a multi-record targets file.
Figure 6 describes the format for a multi-record targets file. The first line of the file is a header that specifies the version of Genfra that produced the file. This line is followed by entries for each molecule in the library. The first record of the entry gives the library label and the number of atoms in the fragment. There is one line for each atom in the fragment that specifies atom number, atom name, accessible surface estimate, number of ludi types for the atom and the list of ludi types.

<run_name>.ludi_pdb, fort.10

This file describes the protein into whose active site Ludi is fitting fragments. The protein is specified by the Receptor Name parameter in the Ludi/Run command. The file is in pdb format and must begin with an ATOM record. No header records are allowed. This file can contain only the portion of the protein that falls with the search sphere specified at run time; it need not contain the entire protein. This file can be read into Insight II with the Ludi/Load command by turning the Load_Reference_Mol parameter on.

The link fort.10 points to the <run_name>.ludi_pdb when Ludi is run in receptor mode (for the <run_name>.ludi_pdb file that is used in active analog mode, see the next section). Standard mode is specified by toggling the Active_Analog parameter to off in the Ludi/Run command.

<run_name>.ludi_pdb, fort.3

This file describes the superimposed ligands for which Ludi is suggesting analogs. The superimposed ligands are members of the assembly specified by the Assembly Name parameter in the Ludi/Run command. The file is in standard pdb format and must begin with an ATOM record. Each ligand is separated from the previous ligand by a TER record. No header records are allowed.

The link fort.3 points to the <run_name>.ludi_pdb file when Ludi is run in active analog mode. Active analog mode is specified by toggling the Active_Analog parameter to on in the Ludi/Run command.

<run_name>.ludi_inhib, fort. 7

This file describes the partially constructed molecule onto which Ludi tries to add fragments. The molecule is specified by the Ligand Spec parameter in the Ludi/Run command. The <run_name>.ludi_inhib file is in standard pdb format and must begin with an ATOM record. No header records are allowed. This file can be read into Insight II with the Ludi/Load command by turning the Load_Ligand parameter on.

The link fort.7 points to the <run_name>.ludi_inhib file when Ludi is run in link mode. Link mode is specified using the Linkage parameter in the Ludi/Run command. Valid values of Linkage for link mode are One, Two, or Specified.

<run_name>.ludi_inp

The Ludi/Run command automatically creates an input file containing the Ludi execution parameters. A typical example of the <run_name>.ludi_inp file follows:


TITLE
CUTOFF   5.000000
XSITE   -1.853000
YSITE   14.311000
ZSITE   16.658001
RMSMAX   0.300000
PRESEL   2.000000
VDWCUT   3.000000
ESCUT    2.500000
ANGMAX   0.000000
IOUT     0
IELEC    1
IDENSL  25
IDENSP  25
IFLAGV   1
ILINK    0
IANALG   0
IBIFUR   0
ICONMI   0
WLINK    1.000000
WLIPO    1.000000
WHBOND   1.000000
INEWSC   0
IMINSC   0
NHITS  999
ITARGT   0



IBINRD   0
IBURID   0
IGROUP   0
INOTGR   0
INOTAT   0
ICAVMX   0
INVERT   0
IROT     0
Every line (with the exception of the TITLE, IOUT and IBINRD lines) corresponds to a parameter in the Ludi/Parameters, Ludi/Run or Ludi/Library_Filter commands.

Table 12. Description of the <run_name>.ludi_inp File (Page 1 of 3)

Token Description
TITLE   This specifies the run name.  
CUTOFF   Radius parameter, Ludi/Run command (default is 5.0Å).  
XSITE, YSITE, ZSITE   Center of Search parameter, Ludi/Run command.  
RMSMAX   Max RMS parameter, Ludi/Run command (default is 0.3Å).  
PRESEL   Preselect parameter, Ludi/Parameters command (default is 2.0).  
VDWCUT   Min Separation parameter, Ludi/Parameters command (default is 3.0Å).  
ESCUT   ES Dist parameter, Ludi/Parameters command (default is 2.5Å).  
ANGMAX   Max Alignment Angle parameter, Ludi/Run command (default is 14.0°).  
IOUT   This controls the amount of output that is written by Ludi to the
<run_name>.ludi_log file. Possible values for IOUT are 0, 1, 2 and 3.
The default value is 0.  
IELEC   Electrostatic_Check parameter, Ludi/Parameters command.
If on (default), then this line is 1. Otherwise, this line is 0.  
IDENSL   Dens L parameter, Ludi/Parameters command (default is 25 sites).  
IDENSP   Dens P parameter, Ludi/Parameters command (default is 25 sites).  
IFLAGV   Aliphatic_Aromatic parameter, Ludi/Parameters command.
If on (default), then this line is 0. Otherwise, this line is 1.  
ILINK   Linkage parameter, Ludi/Run command.
A value of 0 corresponds to Linkage of None. A value of 99 corresponds to Linkage of One. A value of 98 corresponds to Linkage of Two. When Linkage is Specified, the value of ILINK is equal to the number of linkage sites and the ILINK line is followed by the specifications of the linkage sites, one specification per line. For example:   ILINK 3
11 7
12 1
15 2   In this example three link sites are specified. The first link site is the bond formed by atom 11 (which must be hydrogen) and atom 7 from the partially constructed molecule. These atom numbers correspond to the ATOM records in the pdb file of the partially constructed molecule (i.e., the <run_name>.ludi_inhib file).  
IANALG   Active_Analog parameter, Ludi/Run command.
If off (default), then this line is 0. Otherwise, this line is 1.  
IBIFUR   Reject_Bifurcated parameter, Ludi/Parameters command.
If off (default), then this line is 0. Otherwise, this line is 1.  
ICONMI   Min Surf parameter, Ludi/Parameters command (default is 0%).  
WLINK, WLIPO, WHBOND   Link Weight, Lipo Weight, H Bond Weight parameters, Ludi/Parameters command (default for each is 1.00).  
NFITS   Maximum Fits parameter, Ludi/Parameters command default is 5000.  
INEWSC   Scoring Function parameter, Ludi/Parameters command.
if Hbond_lipo, then this line is 0.
if Energy_Estimate, then this line is 1 (default is 1).
if Energy_Estimate_2, then this line is 2.
if Energy_Estimate_3, then this line is 3.  
IMINSC   Minimum Score parameter, Ludi/Parameters command (default is 0).  
MAXHIT   Maximum Hits parameter, Ludi/Parameters command (default is "ALL").  
ITARGT   Targeted_Mode parameter gives the number of target atom specifications that follow. If off (default), this line is 0. If on, this line gives the number of target atom specifications that follow.  
IBINRD   Format of the fragment library. Possible values are 0 (PDB), 2 (Mol file), 3 (binary). The value is determined  
IBURID   No_Unpaired_Polar parameter, Ludi/Parameters command. If on (default), then this line is 1. Otherwise, this line is 0.  
IGROUP, INOTGR, IYESAT, INOTAT   Require_Group List, Reject_Group List, Require_Atom List and Reject_Atom List, Ludi/Library_Filter command. If list is empty (default), this line is 0. Otherwise this line gives the number of list entries to follow.  
ICAVMX   Max Unfilled Cavity parameter, Ludi/Parameters command. If no cavity search is to be done (default), this line is 0. Otherwise, this line gives the maximum allowable cavity size.  
INVERT   Invert parameter, Ludi/Parameters command. If off (default), then this line is 0. Otherwise, this line is 1.  
IROT   Flexible_Fragments parameter, Ludi/Run command. Possible values 0 (None), 1 (One_At_A_Time), and 2 (Two_At_A_Time).  
ISTART   Index of first library entry to fit. Default is 1.  
ISTOP   Index of last library entry to fit. Default is end of library.  
NATMIN   Min number of atoms allowed in a hit. Default is 0.  
NATMAX   Max number of atoms allowed in a hit. Default is 50.  
ICHARG   Required formal charge within fragment. Default is 0.  
BESTSC   Search Type Parameter, Ludi/Parameters command. Possible Values 0 (Fast) and 1 (Best).  

<run_name>.ludi_env

This file contains 2 Unix commands that set environment variables specifying the full pathnames of the library files. The environment variables are accessible only by the background job and cease to exist when the background job completes.

Output Files--Ludi/Run background job

Table 13. Ludi/Run Output Files

Filename1 Runtime Name2 Description
fort.46     Ludi runtime status checking file.  
<run_name>.ludi_int_sites   fort.11   Interaction sites file.  
<run_name>.ludi_pseudo_protein   fort.12   Pseudoprotein file.  
<run_name>.ludi_frag_<xxx>     Ludi fragment files (one for each hit).  
<run_name>.ludi_err   fort.49   Error file.  
<run_name>.ludi_log     Runtime log file.  
<run_name>.ludi_targ_sites   fort.8   Fragment target sites.  
<run_name>.ludi_last     Stores name of last hit file.  
1 The <run_name> is specified by the Run Name parameter in the Ludi/Run command. <xxx> ranges between 001 and 941. The numbering may not be consecutive. <yyy> ranges between 50 and 990.

2 The Runtime Names are the filenames in effect until the Ludi/Run background job concludes successfully. If the job crashes, the fort.* may be left in the run directory. They can be removed using the Unix rm command. When the job finishes the files are automatically renamed with the names listed under Filename.

fort.46

This file exists only while the Ludi/Run background job is executing and contains runtime status information. The contents of this file are printed in the textport when the Background_Job/Completion_Status command is executed. The following is typical of the status information contained in this file:


 LUDI has found        7 molecules so far.
 It has considered      17 ( 1%) molecules from the database.
 The top score so far is  392.

<run_name>.ludi_int_sites, fort.11

This file contains the interaction sites that Ludi used in fitting new fragments. As described in Chapter 2, Theory, an interaction site occurs where a nonbonded interaction is possible. This file is in PDB format and can be read into Insight II with the Ludi/Load command by turning the Load_Interact_Sites parameter on. The fort.11 file produced by the Ludi/Run background job is automatically renamed to <run_name>.ludi_int_sites when the background job completes.

<run_name>.ludi_pseudo_protein, fort.12

This file describes the exclusion shell that Ludi constructs from the active analogs. No fragment will be fit outside of this shell. The file is in PDB format and can be read into Insight II by turning the Load_Pseudo_Protein parameter on in the Ludi/Load command. The fort.12 file produced by the Ludi/Run background job is automatically renamed to <run_name>.ludi_pseudo_protein when the background job completes.

<run_name>.ludi_frag_<xxx>

When the Ludi/Run background job finds a hit, it stores the fragment in a file and scoring information is included as REMARK records in the PDB formatted files (see below) or as a SKP section in the data records of MDL mol formatted files (see below).

The scoring section starts with a SKP record that specifies the number of records to follow. The second record identifies the section as a "Ludi Score and Interaction Summary". The third record gives the total score for the hit.

The fourth record gives an obsolete id number followed by the library label of the hit, the RMS deviation of the hit coordinates from the interaction site coordinates, the number of atoms employed in the fitting, the number of atoms in the hit, the percentage of the hit surface in contact with the receptor, and, if the run is an active analog run, the percentage occupancy of the exclusion shell. The next lines list the receptor atoms with which the hit is interacting for hydrophobic contacts, hydrogen bonds and ionic interactions. For the hydrogen bonds and ionic interactions, the length (Angstroms) and angle (degrees) of the interaction is listed.

The last line of the scoring section lists the obsolete id number, the library label of the hit, the RMS deviation of the hit coordinates from the interaction site coordinates, the number of atoms employed in the fitting, the number of atoms in the hit, the percentage of the hit surface in contact with the receptor, if the run is an active analog run, the percentage occupancy of the exclusion shell, counts of the number of link sites, hydrophobic sites, hydrogen bond sites to which the hit was fit, the total score, the score from the hydrogen bond term, the score from the lipophilic term, the score from the link term, the count of ionic interactions and the score from that term, the count of rotatable bonds and the score from that term, the count of aromatic-aromatic interactions and the score from that term.


REMARK S  SKP    8


REMARK Ludi Score and Interaction Summary


REMARK 436


REMARK   3 G35  0.37  7  12     83


REMARK  hydrophobic contacts:                TRP  215 C


REMARK  hydrogen bonds      :               GLY  219 O     2.09  133.24


REMARK  ionic interactions  :               ASP  189 OD    1.74  161.65


REMARK                                      ASP  189 OD    1.58  160.58


REMARK   3 G35  0.37  7  12    83              0      1      1     436   55  230    0   2  247   0    0   0    0


ATOM      1  C3  G35     1      -0.476  13.060  16.707


ATOM      2  H1  G35     1      -2.110  11.413  14.394


ATOM      3  N1  G35     1      -1.689  12.101  15.028


ATOM      4 2H1  G35     1      -3.124  13.584  13.413


ATOM      5  N1  G35     1      -2.642  14.164  14.108


ATOM      6 1H1  G35     1      -2.666  15.184  14.222


ATOM      7  C2  G35     1      -0.825  11.863  16.093


ATOM      8  C4  G35     1      -1.121  14.076  16.031


ATOM      9  C5  G35     1      -1.852  13.480  15.016


ATOM     10  H2  G35     1      -0.478  10.886  16.396


ATOM     11  H3  G35     1       0.180  13.174  17.558


ATOM     12  H4  G35     1      -1.061  15.131  16.258





Figure yy:





G35


  Insight           3D                             0





 12 12  0  0  0  0              0


   -0.4760   13.0615   16.7074 C   0  0  0  0  0  0


   -2.1115   11.4108   14.3925 H   0  0  0  0  0  0


   -1.6884   12.1017   15.0285 N   0  0  0  0  0  0


   -3.1235   13.5836   13.4129 H   0  0  0  0  0  0


   -2.6422   14.1642   14.1086 N   0  0  0  0  0  0


   -2.6662   15.1841   14.2215 H   0  0  0  0  0  0


   -0.8247   11.8644   16.0939 C   0  0  0  0  0  0


   -1.1205   14.0768   16.0315 C   0  0  0  0  0  0


   -1.8522   13.4809   15.0166 C   0  0  0  0  0  0


   -0.4723   10.8802   16.4028 H   0  0  0  0  0  0


    0.1859   13.1771   17.5657 H   0  0  0  0  0  0


   -1.0650   15.1426   16.2532 H   0  0  0  0  0  0


  1  7  2  0  0  0


  1  8  1  0  0  0


  1 11  1  0  0  0


  2  3  1  0  0  0


  3  7  1  0  0  0


  3  9  1  0  0  0


  4  5  1  0  0  0


  5  6  1  0  0  0


  5  9  1  0  0  0


  7 10  1  0  0  0


  8  9  2  0  0  0


  8 12  1  0  0  0


S  SKP    8


Ludi Score and Interaction Summary


435


 12 G35  0.37  7  12     83


 hydrophobic contacts:                TRP  215 C


 hydrogen bonds      :               GLY  219 O     2.09  133.25


 ionic interactions  :               ASP  189 OD    1.74  161.68


                                     ASP  189 OD    1.58  160.54


 12 G35  0.37  7  12    83              0      1      1     435   55  230    0   2  246   0    0   0    0


M  END


$$$$

The hit files are either PDB or MDL mol format depending on the format of the Ludi library.

<run_name>.ludi_err, fort.49

Fort.49 contains any error messages produced by the Ludi/Run background job. It is automatically renamed to <run_name>.ludi_err.

<run_name>.ludi_log

This file contains information describing the run of the Ludi/Run background job. The fields are self-explanatory and include a list of the runtime parameters, numbers of interaction sites generated and a summary of fitting results for each fragment in the library.

<run_name>.ludi_targ_sites, fort.8

This file contains the list of target atoms for each fragment that was used in fitting to the interaction sites. If the library targets file format was of the single-record type, it will recapitulate what is already in the targets file. If the targets file format was of the multi-record format, this file lists for each fit: the fragment label and the atom name, atom number and type for each target atom.


 AAAA   N   2  -3   C   4   1   C   5   1

Input Files--Ludi/Add_Fragment background job

Table 14. Ludi/Add_Fragment Input Files

Filename Linknamea Description
GENFRA_RUN.pdb_entry   fort.41   Fragment topology, PDB format.  
GENFRA_RUN.sd_entry   fort.41   Fragment topology, MDL mol format.  
GENFRA_RUN.inp     Runtime parameters for Ludi/Add_Fragment background job.  
GENFRA_RUN.env     Library locator file.  
<lib_file.struct>b     Library Structure File (may not exist yet.)  
<lib_file.inp>b     Library Targets File (may not exist yet.)  
aLinknames are runtime links to the files listed under Filename in this table. These links are removed when the Ludi/Add_Fragment background gob completes.   b<lib_file.struct> and <lib_file.inp> are specified in the Ludi/Add_Fragment command by the parameters Structure File and Targets File, respectively.  

GENFRA_RUN.pdb_entry, GENFRA_RUN.sd_entry, fort.41

These files contain the structure of the fragment being added to the library. The structure is in PDB format in GENFRA_RUN.pdb_entry and in MDL mol format in GENFRA_RUN.sd_entry. If the fragment is being added to an existing library, a shell script determines the library format and then links fort.41 to the correspondingly formatted fragment structure file. If a new library is being created, the user has specified the format for the library. All three files are automatically deleted when the Ludi/Add_Fragment background job completes.

GENFRA_RUN.inp

GENFRA_RUN.inp contains the runtime control parameters for the Ludi/Add_Fragment background job. It is deleted automatically when the Ludi/Add_Fragment background job completes.

GENFRA_RUN.env

This file contains 2 Unix commands that set environment variables specifying the full pathnames of the library files. The environment variables are accessible only by the background job and cease to exist when the background job completes. This file is deleted automatically when the Ludi/Add_Fragment background job completes.

<lib_file.struct>, <lib_file.inp>

These files comprise the library to which the fragment is being added. <lib_file.struct> is the structure file and contains the fragment topologies. <lib_file.inp> is the targets file and identifies the functional groups in the fragments that will be fit to interaction sites during a Ludi run.

Output Files--Ludi/Add_Fragment background job

Table 15. Ludi/Add_Fragment Output Files

Filename Description
GENFRA_RUN.log   Runtime log file.  
fort.3   Targets file entry for the new fragment.  
fort.7   Structure file entry for the new fragment.  
<lib_file.struct>   Modified library structure file.  
<lib_file.inp>   Modified library targets file.  

GENFRA_RUN.log

This file contains information describing the run of the Ludi/Add_Fragment background job. At the end of the run, the information is automatically printed in the textport and the file is deleted. The information printed to the textport includes the number of target sites found for the fragment, how many library entries were generated for the fragment and whether adding the new entries to the library was successful.

fort.3

This file contains the targets file entries created by the Ludi/Add_Fragment background job for the new fragment. The contents of the file are appended to <lib_file.inp> and this file is deleted.

fort.7

This file contains the structure file entries created by the Ludi/Add_Fragment background job for the new fragment. The contents of the file are appended to <lib_file.struct> and this file is deleted.

<lib_file.struct>, <lib_file.inp>

These files comprise the library to which the fragment has been added. <lib_file.struct> is the structure file and contains the fragment topologies. <lib_file.inp> is the targets file and identifies the functional groups in the fragments that will be fit to interaction sites during a Ludi run.

Input Files--Ludi/Score background job

Table 16. Ludi/Score Input Files

Filenamea Linknameb Description
<run_name>.ludi_receptor   fort.10   PDB file for the receptor.  
<run_name>.ludi_ligand   fort.9   PDB file for the ligand.  
aThe <run_name> is specified by the Run Name parameter in the Ludi/Score command.   bLink names are runtime links to the files listed under Filename in this table. These links are removed when the Ludi/Score background job completes.  

<run_name>.ludi_receptor, fort.10

This file describes the receptor of the receptor/ligand complex being scored. The file is in PDB format and may not contain the whole receptor but only a zone of receptor atoms surrounding the ligand. Fort.10 is a runtime link to <run_name>.ludi_receptor. Both files are automatically deleted when the Ludi/Score background job completes.

<run_name>.ludi_ligand, fort.9

This file describes the ligand of the receptor/ligand complex being scored. The file is in PDB format. Fort.9 is a runtime link to <run_name>.ludi_ligand. Both files are automatically deleted when the Ludi/Score background job completes.

Output Files--Ludi/Score background job

Table 17. Ludi/Score Output Files

Filenamea Runtime Nameb Description
<run_name>.ludi_score_1   <run_name>.ludi_log _1   Runtime log file.  
  <run_name>.lig_names    
  fort.40    
<run_name>.ludi_score_2   <run_name>.ludi_log_2   <run_name>.lig_names   fort.50    
<run_name>.ludi_score_3   <run_name>.ludi_log_3   <run_name>.lig_names   fort.60    
<run_name>.ludi_err   fort.49   Error file.  
aThe <run_name> is specified by the Run Name parameter in the Ludi/Score command.   bThe Runtime Names are the filenames in effect until the Ludi/Score background job concludes. When the job finishes, the files are automatically compiled and renamed with the names listed under Filename.  

<run_name>.ludi_score_1, <run_name>.ludi_log_1, fort.40;
<run_name>.ludi_score_2, <run_name>.ludi_log_2, fort.50;
<run_name>.ludi_score_3, <run_name>.ludi_log_3, fort.60;

The indices (1, 2, 3) in the above file names correspond to the scoring function selected (Energy_Estimate_1, Energy_Estimate_2 or Energy_Estimate_3).

<run_name>.ludi_score_x is a compilation of the files, <run_name>.ludi_log_x, and <run_name>.lig_names. <run_name>.ludi_log contains information describing the run of the Ludi/Score background job. Fort contains the scoring results and <run_name>.lig_names contains the list of ligands being scored. At the completion of the Ludi/Score background job, the three files are compiled into <run_name>.ludi_score and the constituent files are deleted.

<run_name>.ludi_err, fort.49

Fort.49 contains any error messages produced by the Ludi/Score background job. It is automatically renamed to <run_name>.ludi_err at the end of the job.



Last updated September 01, 1999 at 02:15PM PDT.
Copyright © 1999, Molecular Simulations Inc. All rights reserved.