If the mol2 file has correct connectivity then I would stay with mol2 format.
PDB format has no connectivity and antechamber is forced to generate bonds and
it may not be correct. Both Mercury and Pcmodel had trouble getting a good
connectivity from the pdb input and Chimera was completely unable to deal with
it. I generally use Chimera for doing Dock prep and it will add the hydrogens
and run antechamber to generate a new mol2 file which is compatible with Dock
and should be compatible with Amber.
You can always force bondtype (part of antechamber) to accept the current bond
scheme using the command line(partial rather than full) if you have a good
connectivity.
Kevin
Quoting Jack Shultz <js.drugdiscoveryathome.com>:
> My original mol2 file is compatible with antechamber. Here are two files:1)
> Original mol2 file converted to pdb using antechamber
> [boincadm.vps receptor]$ cat ligand.pdb
> ATOM 1 C LIG 1 0.000 0.000 0.000
> ATOM 2 N LIG 1 0.001 -0.052 1.319
> ATOM 3 C1 LIG 1 1.324 -0.033 1.778
> ATOM 4 C2 LIG 1 2.150 0.034 0.650
> ATOM 5 O LIG 1 1.312 0.054 -0.463
> ATOM 6 C3 LIG 1 3.541 0.067 0.801
> ATOM 7 C4 LIG 1 4.107 0.032 2.082
> ATOM 8 C5 LIG 1 3.281 -0.035 3.210
> ATOM 9 C6 LIG 1 1.889 -0.068 3.058
> ATOM 10 C7 LIG 1 -1.208 0.000 -0.854
> ATOM 11 C8 LIG 1 -1.780 -1.212 -1.259
> ATOM 12 C9 LIG 1 -2.923 -1.212 -2.067
> ATOM 13 C10 LIG 1 -3.495 0.000 -2.471
> ATOM 14 C11 LIG 1 -2.923 1.212 -2.067
> ATOM 15 N1 LIG 1 -3.501 2.438 -2.475
> ATOM 16 C12 LIG 1 -4.399 3.040 -1.701
> ATOM 17 C13 LIG 1 -4.989 4.332 -2.119
> ATOM 18 C14 LIG 1 -6.344 4.404 -2.463
> ATOM 19 C15 LIG 1 -6.902 5.625 -2.858
> ATOM 20 C16 LIG 1 -6.105 6.775 -2.910
> ATOM 21 C17 LIG 1 -4.750 6.703 -2.567
> ATOM 22 C18 LIG 1 -4.191 5.481 -2.171
> ATOM 23 C19 LIG 1 -8.257 5.697 -3.202
> ATOM 24 C20 LIG 1 -9.055 4.547 -3.150
> ATOM 25 C21 LIG 1 -8.497 3.326 -2.754
> ATOM 26 C22 LIG 1 -7.141 3.254 -2.411
> ATOM 27 O1 LIG 1 -4.739 2.525 -0.638
> ATOM 28 C23 LIG 1 -1.780 1.212 -1.259
> ATOM 29 O2 LIG 1 -1.221 -2.399 -0.863
> ATOM 30 H LIG 1 5.180 0.057 2.199
> ATOM 31 H1 LIG 1 3.717 -0.061 4.198
> ATOM 32 H2 LIG 1 1.252 -0.119 3.929
> ATOM 33 H3 LIG 1 4.178 0.118 -0.069
> ATOM 34 H4 LIG 1 -4.376 0.000 -3.095
> ATOM 35 H5 LIG 1 -3.364 -2.148 -2.379
> ATOM 36 H6 LIG 1 -1.339 2.148 -0.947
> ATOM 37 H7 LIG 1 -1.709 -3.153 -1.230
> ATOM 38 H8 LIG 1 -3.231 2.855 -3.355
> ATOM 39 H9 LIG 1 -10.100 4.603 -3.415
> ATOM 40 H10 LIG 1 -9.112 2.439 -2.714
> ATOM 41 H11 LIG 1 -6.711 2.312 -2.106
> ATOM 42 H12 LIG 1 -8.688 6.639 -3.507
> ATOM 43 H13 LIG 1 -4.135 7.590 -2.607
> ATOM 44 H14 LIG 1 -3.146 5.426 -1.906
> ATOM 45 H15 LIG 1 -6.535 7.717 -3.216
>
> 2) Ligand derived from Autodock DLG --> write_lowest_energy_ligand.py -->
> pdbqt_to_pdb.py
> So I am wondering if it is how it is formated or do I just need to add
> additional hydrogens?
>
> [boincadm.vps receptor]$ cat ligand_BE.pdb
> REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0
> ATOM 1 C LIG d 1 -8.534 -6.465 8.983 0.00 0.00 liga
> C
> ATOM 2 C LIG d 1 -8.248 -7.667 8.325 0.00 0.00 liga
> C
> ATOM 3 C LIG d 1 -8.751 -8.875 8.822 0.00 0.00 liga
> C
> ATOM 4 C LIG d 1 -9.541 -8.882 9.977 0.00 0.00 liga
> C
> ATOM 5 C LIG d 1 -9.828 -7.680 10.635 0.00 0.00 liga
> C
> ATOM 6 C LIG d 1 -9.324 -6.472 10.138 0.00 0.00 liga
> C
> ATOM 7 N LIG d 1 -10.626 -7.686 11.804 0.00 0.00 liga
> N
> ATOM 8 C LIG d 1 -10.123 -8.135 12.950 0.00 0.00 liga
> C
> ATOM 9 O LIG d 1 -8.970 -8.559 12.993 0.00 0.00 liga
> O
> ATOM 10 H LIG d 1 -11.578 -7.350 11.767 0.00 0.00 liga
> H
> ATOM 11 C LIG d 1 -10.953 -8.123 14.177 0.00 0.00 liga
> C
> ATOM 12 C LIG d 1 -11.356 -6.906 14.738 0.00 0.00 liga
> C
> ATOM 13 C LIG d 1 -12.139 -6.894 15.897 0.00 0.00 liga
> C
> ATOM 14 C LIG d 1 -10.975 -5.699 14.138 0.00 0.00 liga
> C
> ATOM 15 C LIG d 1 -12.520 -8.101 16.497 0.00 0.00 liga
> C
> ATOM 16 C LIG d 1 -12.542 -5.677 16.458 0.00 0.00 liga
> C
> ATOM 17 C LIG d 1 -12.117 -9.318 15.937 0.00 0.00 liga
> C
> ATOM 18 C LIG d 1 -11.332 -9.330 14.776 0.00 0.00 liga
> C
> ATOM 19 C LIG d 1 -12.162 -4.469 15.859 0.00 0.00 liga
> C
> ATOM 20 C LIG d 1 -11.379 -4.481 14.699 0.00 0.00 liga
> C
> ATOM 21 C LIG d 1 -8.001 -5.188 8.458 0.00 0.00 liga
> C
> ATOM 22 N LIG d 1 -7.961 -4.846 7.184 0.00 0.00 liga
> N
> ATOM 23 C LIG d 1 -7.392 -3.571 7.069 0.00 0.00 liga
> C
> ATOM 24 C LIG d 1 -7.081 -3.141 8.364 0.00 0.00 liga
> C
> ATOM 25 C LIG d 1 -7.116 -2.745 5.971 0.00 0.00 liga
> C
> ATOM 26 O LIG d 1 -7.465 -4.161 9.231 0.00 0.00 liga
> O
> ATOM 27 C LIG d 1 -6.494 -1.886 8.563 0.00 0.00 liga
> C
> ATOM 28 C LIG d 1 -6.218 -1.060 7.466 0.00 0.00 liga
> C
> ATOM 29 C LIG d 1 -6.529 -1.491 6.171 0.00 0.00 liga
> C
> ATOM 30 O LIG d 1 -7.474 -7.661 7.194 0.00 0.00 liga
> O
> ATOM 31 H LIG d 1 -7.534 -6.808 6.735 0.00 0.00 liga
> H
>
>
> On Fri, Jun 19, 2009 at 8:57 AM, <gilbert.bluemarble.net> wrote:
>
> > I was able to read the pdb records into Mercury and write them back out
> as
> > a
> > mol2 file. I was also able to use Pcmodel do the same thing. I was not
> able
> > to
> > read the structure with Chimera.
> >
> > When I look at the mol2 file there are two many double bonds in the
> > aromatic
> > rings which probably means the bond distances are too short which may be
> > the
> > reason antechamber fails.
> >
> > Kevin Gilbert
> > Serena Software
> >
> > Quoting Jack Shultz <js.drugdiscoveryathome.com>:
> >
> > > I'm trying to figure out how to extract a ligand from our docking log
> > > file such that it will be compatible with amber. I grepped the
> > > receptor-ligand complex for just the ligand file and successfully
> > > opened it in PyMole but antechamber is not successful converting to
> > > mol2.
> > >
> > > If I write_all_complexes.py
> > > then grep LIG fzd2_ligand_0.pdbqt > fzd2_ligand_0.pdb
> > >
> > > [boincadm.vps receptor]$ cat fzd2_ligand_0.pdb
> > > ATOM 1 C LIG d 1 -8.564 -6.344 8.959 0.00 0.00
> > 0.052
> > > A
> > > ATOM 2 C LIG d 1 -8.353 -7.525 8.238 0.00 0.00
> > 0.080
> > > A
> > > ATOM 3 C LIG d 1 -8.898 -8.731 8.694 0.00 0.00
> > 0.040
> > > A
> > > ATOM 4 C LIG d 1 -9.656 -8.756 9.871 0.00 0.00
> > 0.032
> > > A
> > > ATOM 5 C LIG d 1 -9.868 -7.575 10.591 0.00 0.00
> > 0.036
> > > A
> > > ATOM 6 C LIG d 1 -9.322 -6.369 10.136 0.00 0.00
> > 0.048
> > > A
> > > ATOM 7 N LIG d 1 -10.633 -7.600 11.782 0.00 0.00
> > -0.323
> > > N
> > > ATOM 8 C LIG d 1 -10.097 -8.061 12.908 0.00 0.00
> > 0.257
> > > C
> > > ATOM 9 O LIG d 1 -8.941 -8.479 12.913 0.00 0.00
> > -0.267
> > > OA
> > > ATOM 10 H LIG d 1 -11.588 -7.268 11.775 0.00 0.00
> > 0.169
> > > HD
> > > ATOM 11 C LIG d 1 -10.892 -8.069 14.157 0.00 0.00
> > 0.043
> > > A
> > > ATOM 12 C LIG d 1 -11.303 -6.861 14.733 0.00 0.00
> > -0.010
> > > A
> > > ATOM 13 C LIG d 1 -12.054 -6.868 15.914 0.00 0.00
> > -0.025
> > > A
> > > ATOM 14 C LIG d 1 -10.962 -5.645 14.127 0.00 0.00
> > 0.013
> > > A
> > > ATOM 15 C LIG d 1 -12.395 -8.083 16.519 0.00 0.00
> > 0.012
> > > A
> > > ATOM 16 C LIG d 1 -12.464 -5.660 16.490 0.00 0.00
> > 0.012
> > > A
> > > ATOM 17 C LIG d 1 -11.984 -9.291 15.944 0.00 0.00
> > 0.002
> > > A
> > > ATOM 18 C LIG d 1 -11.232 -9.284 14.762 0.00 0.00
> > 0.018
> > > A
> > > ATOM 19 C LIG d 1 -12.124 -4.444 15.884 0.00 0.00
> > 0.001
> > > A
> > > ATOM 20 C LIG d 1 -11.373 -4.437 14.703 0.00 0.00
> > 0.001
> > > A
> > > ATOM 21 C LIG d 1 -7.987 -5.069 8.478 0.00 0.00
> > 0.183
> > > A
> > > ATOM 22 N LIG d 1 -7.556 -4.088 9.248 0.00 0.00
> > -0.221
> > > NA
> > > ATOM 23 C LIG d 1 -7.080 -3.046 8.442 0.00 0.00
> > 0.093
> > > A
> > > ATOM 24 C LIG d 1 -7.244 -3.448 7.112 0.00 0.00
> > 0.106
> > > A
> > > ATOM 25 C LIG d 1 -6.522 -1.794 8.732 0.00 0.00
> > 0.034
> > > A
> > > ATOM 26 O LIG d 1 -7.814 -4.719 7.140 0.00 0.00
> > -0.289
> > > OA
> > > ATOM 27 C LIG d 1 -6.851 -2.600 6.070 0.00 0.00
> > 0.040
> > > A
> > > ATOM 28 C LIG d 1 -6.293 -1.348 6.360 0.00 0.00
> > 0.003
> > > A
> > > ATOM 29 C LIG d 1 -6.130 -0.946 7.691 0.00 0.00
> > 0.002
> > > A
> > > ATOM 30 O LIG d 1 -7.610 -7.501 7.086 0.00 0.00
> > -0.360
> > > OA
> > > ATOM 31 H LIG d 1 -7.659 -6.631 6.659 0.00 0.00
> > 0.217
> > > HD
> > > [boincadm.vps receptor]$ antechamber -fi pdb -i fzd2_ligand_0.pdb -fo
> > > mol2 -o fzd2_ligand_0.mol2
> > >
> > > Warning: the assigned bond types may be wrong, please :
> > > (1) double check the structure (the connectivity) and/or
> > > (2) adjust atom valence penalty parameters in APS.DAT, and/or
> > > (3) increase MAXVASTATE in define.h and recompile bondtype.C
> > > (4) increase PSCUTOFF in define.h and recompile bondtype.C
> > > Be cautious, use a large value of PSCUTOFF (>10) will
> > > significantly increase the computer time
> > > Error: cannot run "/usr/local/antechamber-1.27/exe/bondtype -i
> > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
> > > in judgebondtype() of antechamber.c properly, exit
> > > [boincadm.vps receptor]$
> > >
> > >
> > > --
> > > Jack
> > >
> > > http://drugdiscoveryathome.com
> > > http://hydrogenathome.org
> > >
> > >
> > >
> > > --
> > > Jack
> > >
> > > http://drugdiscoveryathome.com
> > > http://hydrogenathome.org
> > >
> > >
> > >
> > > --
> > > Jack
> > >
> > > http://drugdiscoveryathome.com
> > > http://hydrogenathome.org
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 06 2009 - 10:08:29 PDT
