AMBER Archive (2009)

Subject: [AMBER] From DLG to Antechamber

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Thu Jun 18 2009 - 19:04:15 CDT

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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