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.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]$
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Received on Mon Jul 06 2009 - 10:06:50 PDT
