AMBER Archive (2009)
Subject: Re: [AMBER] From DLG to Antechamber

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Fri Jun 19 2009 - 09:34:33 CDT

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Looks like I just needed to add hydrogens using Babel. thanks for the help!

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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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-- Jack

http://drugdiscoveryathome.com http://hydrogenathome.org

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AMBER Archive (2009)Subject: Re: [AMBER] From DLG to Antechamber

AMBER Archive (2009)
Subject: Re: [AMBER] From DLG to Antechamber