Dear list,
I am a little bit worried.
If I start from the conformer given at the end of this message,
MMFF94 gives me a minimized conformer energy of -122.528
while UFF gives me 69.098 (I assume, both are in kcal/mol).
I am a little bit annoyed by the fact that the UFF energy
is not even negative and that the two FFs disagree by so much.
Are the two FFs using different units?
Do the two FFs compute something different?
I used the following python code for conformer minimization:
---
def minimize_conformer(ff, mol):
# ligand is supposed to be already properly protonated
# for given pH and in 3D
assert(mol.GetNumConformers() == 1)
conv_ene = []
if ff == "uff":
conv_ene = AllChem.UFFOptimizeMoleculeConfs(mol)
elif ff == "mmff":
conv_ene = AllChem.MMFFOptimizeMoleculeConfs(mol)
else:
print("minimize_conformer: unsupported FF: %s" % ff,
file=sys.stderr)
assert(False)
not_converged, ene = conv_ene[0]
assert(not_converged == 0)
return (mol, ene)
---
--- mol2
@<TRIPOS>MOLECULE
caffeine
24 25 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 5.1112 0.7768 -0.9264 C.2 1 <0>
0.0365
2 C2 3.6441 2.3853 -1.2367 C.2 1 <0>
-0.2366
3 C3 3.0449 1.2362 -0.7981 C.2 1 <0>
0.2902
4 C4 2.9523 3.5995 -1.5265 C.2 1 <0>
0.7150
5 C5 0.8629 2.2904 -0.8430 C.2 1 <0>
0.6900
6 C6 6.0477 2.9539 -1.7310 C.3 1 <0>
0.2556
7 C7 1.0831 -0.0921 -0.1245 C.3 1 <0>
0.3001
8 C8 0.7590 4.6603 -1.5747 C.3 1 <0>
0.3001
9 N1 3.9557 0.2327 -0.6044 N.2 1 <0>
-0.5653
10 N2 4.9734 2.0838 -1.3171 N.pl3 1 <0>
0.0476
11 N3 1.6743 1.1555 -0.5931 N.am 1 <0>
-0.4231
12 N4 1.5557 3.4679 -1.3036 N.am 1 <0>
-0.4201
13 O1 3.5018 4.6256 -1.9190 O.2 1 <0>
-0.5700
14 O2 -0.3616 2.2696 -0.6756 O.2 1 <0>
-0.5700
15 H1 6.0715 0.2803 -0.8973 H 1 <0>
0.1500
16 H2 6.1690 2.8492 -2.8124 H 1 <0>
0.0000
17 H3 5.7997 3.9871 -1.4724 H 1 <0>
0.0000
18 H4 6.9664 2.6656 -1.2124 H 1 <0>
0.0000
19 H5 1.0630 -0.0986 0.9753 H 1 <0>
0.0000
20 H6 0.0567 -0.1790 -0.5104 H 1 <0>
0.0000
21 H7 1.6835 -0.9404 -0.4850 H 1 <0>
0.0000
22 H8 0.4310 4.6518 -2.6246 H 1 <0>
0.0000
23 H9 -0.1216 4.6705 -0.9156 H 1 <0>
0.0000
24 H10 1.3672 5.5577 -1.3880 H 1 <0>
0.0000
@<TRIPOS>BOND
1 1 9 2
2 1 10 1
3 2 3 2
4 2 4 1
5 2 10 1
6 3 9 1
7 3 11 1
8 4 12 am
9 4 13 2
10 5 11 am
11 5 12 am
12 5 14 2
13 6 10 1
14 7 11 1
15 8 12 1
16 1 15 1
17 6 16 1
18 6 17 1
19 6 18 1
20 7 19 1
21 7 20 1
22 7 21 1
23 8 22 1
24 8 23 1
25 8 24 1
---
Regards,
F.
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