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"obconformer" - Generate Best Conformer
What Is "obconformer" command? How to use it to generate the best conformer from a base molecule?
✍: FYIcenter.com
"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:
Open conformer.svg in a Web browser to compare the best conformer with the base molecule:
⇒ "obenergy" - Calculate Molecule Energy
2020-11-22, 1354🔥, 0💬
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