Sorry for bothering. A regression appears to have been crept in the
current SVN OpenBabel; if you issue:
obenergy -ff MMFF94 test.mol2
with the attached mol2 file, you get output1.txt (wrong), while until
about 2 weeks ago you could get the correct output (output2.txt).
I can give you some more details which maybe help: if you convert this
.mol2 format to .sdf with babel, you get an additional line before 'M END':
M ISO 8 3 2 4 2 5 2 6 2 7 2 8 2 9 2 10 2
So this indicates that all hydrogens are perceived as deuterium atoms
(see type "D" in output1.txt), hence the inability to assign correct
MMFF types.
Thanks, bye
Paolo
--
==========================================================
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Department of Drug Science Fax: +39 011 6707687
and Technology Mob: +39 348 5537206
Via Pietro Giuria, 9
10125 Torino, Italy
E-mail: [email protected] http://open3dqsar.org
==========================================================
obenergy: could not setup force field.
A T O M T Y P E S
IDX TYPE
1 1
2 3
3 D
4 D
5 D
6 D
7 D
8 8
9 6
10 7
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 0.000000
P A R T I A L C H A R G E S
IDX CHARGE
1 0.331000
2 0.659000
3 0.253000
4 0.253000
5 0.000000
6 0.000000
7 0.243000
8 -0.776000
9 -0.393000
10 -0.570000
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 1-5 (IDX)...
USING EMPIRICAL RULE FOR BOND STRETCHING 1-6 (IDX)...
USING EMPIRICAL RULE FOR BOND STRETCHING 3-8 (IDX)...
USING EMPIRICAL RULE FOR BOND STRETCHING 4-8 (IDX)...
USING EMPIRICAL RULE FOR BOND STRETCHING 7-9 (IDX)...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 2-1-5 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 2-1-6 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 5-1-6 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 5-1-8 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 6-1-8 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 1-8-3 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 1-8-4 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 3-8-4 (IDX)...
USING EMPIRICAL RULE FOR ANGLE BENDING FORCE CONSTANT 2-9-7 (IDX)...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
COULD NOT FIND VAN DER WAALS PARAMETERS FOR 1-7 (IDX)...
A T O M T Y P E S
IDX TYPE
1 1
2 3
3 23
4 23
5 5
6 5
7 24
8 8
9 6
10 7
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 0.000000
P A R T I A L C H A R G E S
IDX CHARGE
1 0.331000
2 0.659000
3 0.360000
4 0.360000
5 0.000000
6 0.000000
7 0.500000
8 -0.990000
9 -0.650000
10 -0.570000
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...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...
E N E R G Y
TOTAL BOND STRETCHING ENERGY = 0.55684 kcal/mol
TOTAL ANGLE BENDING ENERGY = 1.38450 kcal/mol
TOTAL STRETCH BENDING ENERGY = 0.24423 kcal/mol
TOTAL TORSIONAL ENERGY = -4.71331 kcal/mol
TOTAL OUT-OF-PLANE BENDING ENERGY = 0.00000 kcal/mol
TOTAL VAN DER WAALS ENERGY = 2.78652 kcal/mol
TOTAL ELECTROSTATIC ENERGY = 26.61544 kcal/mol
TOTAL ENERGY = 26.87422 kcal/mol
@<TRIPOS>MOLECULE
AGLYSL01
10 9 1 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 -1.6234 1.6965 8.8431 C.3 1 AGLY 0.3310
2 C2 -1.5438 0.1710 8.8960 C.2 1 AGLY 0.6590
3 H1 -1.5827 1.7640 6.8094 H 1 AGLY 0.3600
4 H3 -0.1271 1.8630 7.4736 H 1 AGLY 0.3600
5 H5 -2.6707 1.9987 8.9343 H 1 AGLY 0.0000
6 H6 -1.0462 2.1092 9.6756 H 1 AGLY 0.0000
7 H7 -2.3655 0.3289 10.6732 H 1 AGLY 0.5000
8 N1 -1.0818 2.2182 7.5784 N.3 1 AGLY -0.9900
9 O5 -2.0344 -0.3437 10.0478 O.3 1 AGLY -0.6500
10 O6 -1.0893 -0.5326 8.0048 O.2 1 AGLY -0.5700
@<TRIPOS>BOND
1 1 2 1
2 1 5 1
3 1 6 1
4 1 8 1
5 2 9 1
6 2 10 2
7 3 8 1
8 4 8 1
9 7 9 1
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