Hi,
For computing partial charges, starting from mol2, I wonder if I'm doing
well, or if obabel (2.3.2, Linux) has a bug when reading mol2.
E.g. starting from methanoic acid (mol2), with formal charge *(*I tried
with no charge, ending in the same results) :
@<TRIPOS>MOLECULE
methanoate
4 3 1 2 0
SMALL
FORMAL_CHARGES
@<TRIPOS>ATOM
1 H1 -1.7886 -1.3585 2.4295 H 1 <1>
0.0000
2 C -2.4857 -0.5988 2.7802 C.2 1 <1>
0.0000
3 O -3.6856 -0.7978 2.6814 O.co2 1 <1>
-0.5000
4 O -2.0112 0.5272 3.3075 O.co2 1 <1>
-0.5000
@<TRIPOS>BOND
1 2 1 1
2 2 3 ar
3 2 4 ar
I would like to compute the partial charges:
obabel methanoate.mol2 -O methanoate_bab.mol2 # does nothing. Ok.
obabel methanoate.mol2 -O methanoate_bab.sdf # loss of formal charge, no
line "M CHG" in sdf. Using option -p 7 produces the line "M CHG" with the
negative charge, but this option may change the some amine protonation
state in an unwanted way sometimes).
With the produced sdf:
obabel methanoate_bab.sdf -Omethanoate_bab.mol2 # compute wrong partial
charges (around -0.25 for each O.co2, the sum of partial charges is equal
to 0) (but well, OK, there is not negatively charged atom in the sdf file.
If a line like "M CHG 1 3 -1" is present, all is well when converting
from sdf to mol2).
And doing
obabel methanoate.mol2 -O methanoate_bab.mol2 --partialcharge
computes irrelevant partial charges (and the sum of partial charges is
still equal to 0, not -1):
@<TRIPOS>MOLECULE
methanoate
4 3 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 H -1.7886 -1.3585 2.4295 H 1 LIG1 -0.5746
2 C -2.4857 -0.5988 2.7802 C.2 1 LIG1 2.0439
3 O -3.6856 -0.7978 2.6814 O.co2 1 LIG1 -0.7801
4 O -2.0112 0.5272 3.3075 O.co2 1 LIG1 -0.6892
Does obabel consider formal charges (or the FORMAL_CHARGES line) in the
mol2 file or is there an option I have missed?
Regards,
Pascal
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