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
>
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Received on Mon Jul 06 2009 - 10:07:44 PDT
