"obconformer" - Generate Best Conformer

Q

What Is "obconformer" command? How to use it to generate the best conformer from a base molecule?

✍: FYIcenter.com

A

"obconformer" command is a command line tool provided in the Open Babel package that allows you to generate the best conformer from a base molecule.

Here is the user manual of the "obconformer" command.

NAME
     obconformer -- generate conformer coordinates

SYNOPSIS
     obconformer # of conformers # of optimization steps filename

DESCRIPTION
     The obconformer tool can be used as part of a conformational study by 
     generating random conformers using a Monte Carlo search. The best conformer 
     out of the batch of conformers will be output, after taking the supplied number
     of geometry optimization steps. By default, obconformer uses the MMFF94 
     force field.

EXAMPLES
           obconformer 250 100 baseconformer.sdf >rotamer1.sdf

     Generate the best conformer (out of 250) of baseconformer.sdf and write it 
     to rotamer1.sdf after 100 geometry
     optimization steps

Here is an example of generating best conformer using the "obconformer" command.

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o sdf -O tyrosine.sdf --gen2D 
1 molecule converted

fyicenter$ obconformer 250 100  tyrosine.sdf > conformer.sdf

A T O M   T Y P E S
IDX  TYPE
1  37
2  37
3  37
4  37
5  37
6  37
7  4
8  2
9  41
10  32
11  32
12  8
13  35

F O R M A L   C H A R G E S
IDX  CHARGE
1  0.000000
2  0.000000
3  0.000000
4  0.000000
5  0.000000
6  0.000000
7  0.000000
8  0.000000
9  0.000000
10  -0.500000
11  -0.500000
12  0.000000
13  -1.000000

P A R T I A L   C H A R G E S
IDX  CHARGE
1  0.000000
2  0.000000
3  -0.171000
4  0.000000
5  0.000000
6  0.073000
7  -0.138000
8  -0.067000
9  1.050000
10  -0.900000
11  -0.900000
12  -0.118000
13  -0.829000

S E T T I N G   U P   C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
   USING EMPIRICAL RULE FOR BOND STRETCHING 8-12 (IDX)...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
   USING EMPIRICAL RULE FOR ANGLE BENDING 6-7-8 (IDX)...
   USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 6-7-8 (IDX)...
   USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 7-8-9 (IDX)...
   USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 7-8-12 (IDX)...
   USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 9-8-12 (IDX)...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...

W E I G H T E D   R O T O R   S E A R C H
  NUMBER OF ROTATABLE BONDS: 3
  NUMBER OF POSSIBLE ROTAMERS: 480
  INITIAL WEIGHTING OF ROTAMERS...

  GENERATED 250 CONFORMERS

CONFORMER     ENERGY
--------------------
     1        90.092
     2        90.185
     3        90.501
     4        92.225
     5        90.318
     ...

   248        90.255
   249        90.081
   250        90.106

LOWEST ENERGY:   90.077

C O N J U G A T E   G R A D I E N T S

STEPS = 100
STEP n     E(n)       E(n-1)    
--------------------------------
 1      90.077      90.077
10      90.077      90.076
20      90.077      90.077
30      90.077      90.076
40      90.076      90.076
50      90.077      90.076
60      90.076      90.076
70      90.076      90.076
80      90.076      90.075
90      90.077      90.076
100      90.076      90.075

Now generate SVG pictures for both the conformer and the base molecule.

fyicenter$ babel tyrosine.sdf tyrosine.svg  
1 molecule converted
29 audit log messages 

fyicenter$ babel conformer.sdf conformer.svg
1 molecule converted
33 audit log messages 

Open tyrosine.svg in a Web browser to see the base molecule structure:

Tyrosine Molecule
Tyrosine Molecule

Open conformer.svg in a Web browser to compare the best conformer with the base molecule:

Best Conformer of Tyrosine Molecule
Best Conformer of Tyrosine Molecule

 

"obenergy" - Calculate Molecule Energy

"obchiral" - Print Chirality Information

Other Open Babel Commands

⇑⇑ Open Babel Tutorials

2020-11-22, 539👍, 0💬