AMBER Archive (2009)

Subject: Re: [AMBER] From DLG to Antechamber

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Fri Jun 19 2009 - 09:21:37 CDT

The reason for taking the ligand from the docking complex is theoretically
it is positioned at a binding site. So if there is a way of positioning the
original mol2 file at that binding site downstream, that could be a work
around.

On Fri, Jun 19, 2009 at 10:17 AM, <gilbert_at_bluemarble.net> wrote:

> 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_at_drugdiscoveryathome.com>:
>
> > My original mol2 file is compatible with antechamber. Here are two
> files:1)
> > Original mol2 file converted to pdb using antechamber
> > [boincadm_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jack
> >
> > http://drugdiscoveryathome.com
> > http://hydrogenathome.org
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber