On Thu, Jun 20, 2019, Hira Jabeen wrote:
> I don't understand why antechamber changes atoms name and
> arrangement in mol2
It doesn't change atoms names unless you have duplicate atom names in
the same residue. Then antechamber tries to make each atom name unique.
>Like, this is pdb file:
>HETATM 4017 HO72 SFR A 269 22.818 12.980 10.549 0.84 36.34 H
>HETATM 4018 HO62 SFR A 269 21.824 15.969 6.233 0.84 37.27 H
>HETATM 4019 HO31 SFR A 269 18.325 17.622 12.473 0.84 26.32 H
>HETATM 4020 H62B SFR A 269 24.127 13.353 8.201 0.84 37.22 H
>HETATM 4021 H62A SFR A 269 22.801 12.946 7.085 0.84 37.22 H
>HETATM 4022 H17A SFR A 269 19.459 22.308 7.884 0.84 46.88 H
>HETATM 4023 H16A SFR A 269 20.971 22.079 9.766 0.84 46.47 H
>HETATM 4024 H15A SFR A 269 20.450 20.229 10.526 0.84 45.48 H
>And this is mol2:
> 17 C17 20.2460 21.5770 7.6980 c3 301 SFR 0.123600
> 18 O18 19.7130 20.2900 7.3990 os 301 SFR -0.407600
> 19 O32 17.6250 17.4610 10.3710 o 301 SFR -0.482300
> 20 O31 19.1320 17.4760 11.9360 o 301 SFR -0.482300
> 21 H6 21.1830 14.7760 8.2140 hc 301 SFR 0.142700
> 22 H4 21.3740 16.5880 10.8730 hn 301 SFR 0.376700
> 23 H5 22.8750 17.1310 8.9520 h2 301 SFR 0.184700
> 24 H2 18.9100 17.7500 7.8870 h1 301 SFR 0.171700
In what way does the mol2 file come from the pdb file? Exactly what
commands did you give to antechamber? The (partial?) PDB file you list
has only hydrogen atoms, whereas the (partial) mol2 file has carbon,
oxygen and hydrogens. I think we would need to see the complete PDB
file you used (remember that antechamber only takes *single* residues,
not multiple ones), the arguments to antechamber, and the output mol2
file, in order to provide any help.
....dac
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Received on Thu Jun 20 2019 - 07:00:03 PDT
