AMBER Archive (2009)

Subject: Re: [AMBER] From DLG to Antechamber

From: gilbert_at_bluemarble.net
Date: Fri Jun 19 2009 - 07:57:04 CDT


  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
>
> _______________________________________________
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>

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