Hi,
the PDB format doesn't support partial charges, so I suspect the one you write
is not a standard one and will not be recognized by the OpenBabel parser.
Therefore, when generating the Mol2 file, the default charges (Gasteiger, I
believe) will be assigned.
My advice would be to convert directly the MOPAC output (which is supported)
into Mol2, and see if the proper charges are kept.
S
--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
________________________________________
From: samdani [samdani1...@gmail.com]
Sent: Saturday, August 06, 2016 1:07 AM
To: openbabel-discuss@lists.sourceforge.net
Subject: [Open Babel] Atomic charge changed during conversion from pdb to
mol2
Dear open babel community
I used MOPAC to minimize the ligand and obtain the output in PDB format with
atomic charges. When I converted the PDB file to mol2 using babel the atomic
charges were found to be modified. Can anyone help me to preserve the
charges during conversion or any other mode of way to obtain the ligand
output with atomic charges preserved? Below am pasting the PDB file and mol2
file for reference.
The PDB file
ATOM 1 O LIG A 1 -2.264 -1.020 0.122 1.00 -0.39
PROT O
ATOM 2 O LIG A 1 2.796 0.538 -0.113 1.00 -0.39 PROT
O
ATOM 3 C LIG A 1 -1.114 -0.659 0.066 1.00 0.41
PROT C
ATOM 4 C LIG A 1 -0.751 0.792 -0.005 1.00 0.00
PROT C
ATOM 5 C LIG A 1 0.001 -1.641 0.066 1.00 -0.22
PROT C
ATOM 6 C LIG A 1 0.532 1.171 -0.065 1.00 -0.28
PROT C
ATOM 7 C LIG A 1 1.275 -1.250 0.008 1.00 -0.20
PROT C
ATOM 8 C LIG A 1 1.640 0.192 -0.062 1.00 0.43
PROT C
ATOM 9 C LIG A 1 -1.893 1.734 -0.003 1.00 -0.45
PROT C
ATOM 10 H LIG A 1 -0.305 -2.687 0.117 1.00 0.18
PROT H
ATOM 11 H LIG A 1 0.839 2.216 -0.119 1.00 0.19
PROT H
ATOM 12 H LIG A 1 2.118 -1.944 0.006 1.00 0.18
PROT H
ATOM 13 H LIG A 1 -2.493 1.632 0.919 1.00 0.18
PROT H
ATOM 14 H LIG A 1 -1.591 2.787 -0.085 1.00 0.16
PROT H
ATOM 15 H LIG A 1 -2.589 1.523 -0.834 1.00 0.18
PROT H
END
Converted mol2 file using babel
@<TRIPOS>MOLECULE
A_lig1.pdb
15 15 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O -2.2640 -1.0200 0.1220 O.2 1 LIG1 -0.2876
2 O 2.7960 0.5380 -0.1130 O.2 1 LIG1 -0.2879
3 C -1.1140 -0.6590 0.0660 C.2 1 LIG1 0.1821
4 C -0.7510 0.7920 -0.0050 C.2 1 LIG1 -0.0002
5 C 0.0010 -1.6410 0.0660 C.2 1 LIG1 -0.0111
6 C 0.5320 1.1710 -0.0650 C.2 1 LIG1 -0.0084
7 C 1.2750 -1.2500 0.0080 C.2 1 LIG1 -0.0113
8 C 1.6400 0.1920 -0.0620 C.2 1 LIG1 0.1795
9 C -1.8930 1.7340 -0.0030 C.3 1 LIG1 -0.0360
10 H -0.3050 -2.6870 0.1170 H 1 LIG1 0.0657
11 H 0.8390 2.2160 -0.1190 H 1 LIG1 0.0659
12 H 2.1180 -1.9440 0.0060 H 1 LIG1 0.0657
13 H -2.4930 1.6320 0.9190 H 1 LIG1 0.0279
14 H -1.5910 2.7870 -0.0850 H 1 LIG1 0.0279
15 H -2.5890 1.5230 -0.8340 H 1 LIG1 0.0279
@<TRIPOS>BOND
1 15 9 1
2 11 6 1
3 2 8 2
4 14 9 1
5 6 8 1
6 6 4 2
7 8 7 1
8 4 9 1
9 4 3 1
10 9 13 1
11 12 7 1
12 7 5 2
13 3 5 1
14 3 1 2
15 5 10 1
--
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http://forums.openbabel.org/Atomic-charge-changed-during-conversion-from-pdb-to-mol2-tp4659430.html
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