Re: [AMBER] Fw: parameterization of ligand+protein complex

From: David Case <david.case.rutgers.edu>
Date: Thu, 20 Jun 2019 13:37:06 +0000

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
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