Are you perhaps thinking of the pdbqt format?
On 6 Aug 2016 5:20 p.m., "Stefano Forli" <fo...@scripps.edu> wrote:
> 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
>
>
>
> --
> View this message in context: http://forums.openbabel.org/At
> omic-charge-changed-during-conversion-from-pdb-to-mol2-tp4659430.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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>
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