1.5 LOG FILE AND OUTPUT FILE

 
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N E W L E A D   Mar  1 16:19:05 1997

 ********* NEWLEAD InsightII interface *********
4          OH orientations
4          NH(2) orientations
6          CH(3) orientations
1.5        Scaling factor for vector pair distances
120        Maximum angle in a vector pair
1          Max. error on vector pair distances
15         Max. error on vector pair angles
0.3        Max. superposition RMS deviation
0.1        Max. error on bond lengths
1.5        Max. movement of a fragment atom (A)
0.7        Van der Waals overlap scaling factor
10         Forbidden atom pairs (see manual)
 2,9 3,9 4,9 3,3 6,6 6,9 6,10 9,9 9,10 10,10

 OPTIONS:

 FILES:

 input           [-i] nld.hiv.inp
 output          [-o] nld.out
 log             [-l] nld.log
 preferences     [-p] nld.hiv.prf

 LIBRARIES:

 default library used in all passes

 RECEPTOR:

 1843 atoms found
   99 atoms kept for the van der Waals check
  4.2 to 12.9 A distance range from the ligand C.o.M.
   21 donor and 30 acceptor H-bond centres kept

 I N P U T -> 3 fragments; 27 atoms

 Fragment # 1: C(6)H(6) ->                  12 atoms
 Fragment # 2: C(6)H(6) ->                  12 atoms
 Fragment # 3: H(2)O ->                      3 atoms

   2 donor and 1 acceptor H-bond centres found

 O U T P U T

 20 results found

  N. (dup.) Atm. VdW RMS  Spacer(s)

   1        23    0.000   methylsulfone+M
..........................ethanethiol+A

   2        20    0.000   ethane+M
..........................ethanethiol+M

   3        21    0.000   ethane+M
..........................ethanethiol+A

   4        22    0.000   methylsulfone+M
..........................ethanethiol+M

   5 (  3)  21    0.000   ethanethiol+M
..........................ethanethiol+A

   6 (  2)  20    0.000   ethanethiol+M
..........................ethanethiol+M
[...]
  17 (  2)  20    0.238   ethane+M
..........................ethanethiol+O

  18 (  4)  22    0.265   methylsulfone+M
..........................ethanethiol+O

  19        21    0.309   acetaldehyde_2+M
..........................C-C-bond-added+M

  20        21    0.391   C-C-bond-added+M
..........................acetaldehyde_1+M


 11 structures were written on the output file:

   1/11     methylsulfone+M ethanethiol+A
   2/11     ethane+M ethanethiol+M
   3/11     ethane+M ethanethiol+A
   4/11     methylsulfone+M ethanethiol+M
   5/11     ethanethiol+M ethanethiol
   6/11     ethanethiol+M methylsulfone
   7/11     methylsulfone+M methylsulfone
   8/11     methylsulfone+M ethanethiol
   9/11     ethanethiol+M ethanethiol+O
  10/11     acetaldehyde_2+M C-C-bond-added+M
  11/11     C-C-bond-added+M acetaldehyde_1+M


 CPU time 25 s

Fig. 5

The log file (default name "nld.log") reports on the NEWLEAD run. A sample log file is given in Fig. 5. A description of this file is given below (of course, the line numbers vary for different runs).

line 1      Date and time of the run
lines 3-30    Preferences, options, and files used
lines 31-37    Information on the receptor (if applicable)
lines 38-44    Information on the input fragments
line 48    Number of results
lines 50-114  Summary of all the solutions found. The solutions are ordered according to increasing values of the Van der Waals radii error. The data for each solution is
  • number of the solution in the list, header "N"
  • "parent" molecule for duplicated solutions, header "(dup.)": the number of the first solution in a group of duplicates
  • number of atoms (fragments + spacers), header "Atm."
  • RMS deviation from the Van der Waals radii sums, header "VDW RMS". The RMS deviation is calculated for each spacer and summed over all spacers
  • spacers used, and single-atom spacers, if any, header "Spacer(s)". The single-atom spacers are indicated by the symbols, "+M" (methyl), "+O" (OH), and "+A" (NH2)
lines 117-end  list of the solution as they appear on the output file.


Fig. 6

The output file contains all the results in sorted order. It is written in the same format used for the input file (Columbia, CAR-archive, or MOL2) [2].

In a Columbia output file, the header for each structure contains the number of atoms, the number of the structure and the total number of solutions, the names of the spacers used, and the single-atom spacer(s) used for connection, if any. For instance, the header for the 15th solution of a given run may look like:

 

35 15/34 pyrazine aniline+M

where 35 is the number of atoms and 15/34 indicates that this is the solution 15 out of 34. Pyrazine (as fused ring) and aniline were used as spacers, and a methyl group was attached to aniline. On the computer screen this solution may look as in Fig. 6. The Carbon atoms on the spacers are highlighted in white, while the Carbon atoms on the input fragments retain their standard color. The heterotatoms on the spacers are colored normally.

Accelrys interface To read the solutions in, activate the command Get (Molecule menu), and enter the name of the output file. If a receptor was used, and it is still displayed on your screen, you may find useful to select the "Reference Object" option, and to enter the name of the receptor (or of any fragment). This ensures that the solutions are properly aligned to the receptor.