AMBER Archive (2009)

Subject: Re: [AMBER] From DLG to Antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 19 2009 - 04:26:46 CDT

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]$

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