AMBER Archive (2009)

Subject: Re: [AMBER] From DLG to Antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 19 2009 - 10:54:05 CDT

Jack,

In a FF library two atoms belonging to a same residue cannot have the
same atom name. => I edited your PDB file to make all the atom names
different.

LEaP deals with FF library; this makes it different from other viewers
such as VMD. By comparison load in LEaP your original PDB file => only
few atoms are displayed (because they all have the same name)

ATOM 1 C1 LIG 1 -8.564 -6.344 8.959
ATOM 2 C2 LIG 1 -8.353 -7.525 8.238
ATOM 3 C3 LIG 1 -8.898 -8.731 8.694
ATOM 4 C4 LIG 1 -9.656 -8.756 9.871
ATOM 5 C5 LIG 1 -9.868 -7.575 10.591
ATOM 6 C6 LIG 1 -9.322 -6.369 10.136
ATOM 7 N7 LIG 1 -10.633 -7.600 11.782
ATOM 8 C8 LIG 1 -10.097 -8.061 12.908
ATOM 9 O9 LIG 1 -8.941 -8.479 12.913
ATOM 10 H10 LIG 1 -11.588 -7.268 11.775
ATOM 11 C11 LIG 1 -10.892 -8.069 14.157
ATOM 12 C12 LIG 1 -11.303 -6.861 14.733
ATOM 13 C13 LIG 1 -12.054 -6.868 15.914
ATOM 14 C14 LIG 1 -10.962 -5.645 14.127
ATOM 15 C15 LIG 1 -12.395 -8.083 16.519
ATOM 16 C16 LIG 1 -12.464 -5.660 16.490
ATOM 17 C17 LIG 1 -11.984 -9.291 15.944
ATOM 18 C18 LIG 1 -11.232 -9.284 14.762
ATOM 19 C19 LIG 1 -12.124 -4.444 15.884
ATOM 20 C20 LIG 1 -11.373 -4.437 14.703
ATOM 21 C21 LIG 1 -7.987 -5.069 8.478
ATOM 22 N22 LIG 1 -7.556 -4.088 9.248
ATOM 23 C23 LIG 1 -7.080 -3.046 8.442
ATOM 24 C24 LIG 1 -7.244 -3.448 7.112
ATOM 25 C25 LIG 1 -6.522 -1.794 8.732
ATOM 26 O26 LIG 1 -7.814 -4.719 7.140
ATOM 27 C27 LIG 1 -6.851 -2.600 6.070
ATOM 28 C28 LIG 1 -6.293 -1.348 6.360
ATOM 29 C29 LIG 1 -6.130 -0.946 7.691
ATOM 30 O30 LIG 1 -7.610 -7.501 7.086
ATOM 31 H31 LIG 1 -7.659 -6.631 6.659

Then, I loaded the molecule in xleap, create the bond
(bondbydistance), then do "Unit/add H" & build. You get two much Hs
because the FF atom types are not described.

=> You can use Erase or Draw to modify the hydrogens

=> Edit/Relax selection to remove bump (better low a FF before)

You can do many structure modifications in XLEaP; you just need to
spend time on it... Using XLEaP and a text editor under linux, you can
more or less contruct all the structures you wish.

regards, Francois

> Hi Francois,
> I converted the original molecule in mol2 format to pdb using antechamber
> and it produces this file.
>
> [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
>
> I converted the docking complex to pdbqt, then to pdb using the autodock
> scripts
>
> [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
> TER 32 LIG d 1
> [boincadm_at_vps receptor]$
>
>
>
>
> On Fri, Jun 19, 2009 at 5:26 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
>> Dear Jack,
>>
>> After a quick look, it seems you need to add the hydrogens to your
>> structure.
>>
>> regards, Francois
>>
>>
>>
>> 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]$
>>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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