Ligand minimization Using prodrg
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6.2 years ago
pinke ▴ 10

I tried to optimize ligands using prodrg. after the completion of energy minimization , I choosed DRGFIN.PDB file of ligand, as its having all hydrogens added. when i tried to upload this ligand in autodock for docking purpose its always displaying an error "unknown ligand file type pdb " for all the ligands which i have minimized using prodrg . please kindly help me in resolving this issue. Thank you

Drug designing docking ligand preparation cadd • 2.4k views
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Entering edit mode
6.2 years ago
João Rodrigues ★ 2.5k

A long shot, but is the file extension uppercase? Try lowercase. Otherwise, look in the documentation if you need to add parameters or topology files to Autodock somehow.

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6.2 years ago
pinke ▴ 10

thanks for replying, yeah i tried to change the cases, and even name too. there is no change, still getting same error. these are the coordinates of the energy minimized ligand ( DRGFIN.PDB ). please kindly have a look on this. and please tell me if there is anything to be corrected here. Thanks in advance.

------------------------------------------------------------------------------

REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAE LIG     1      -0.980   1.430   0.000  1.00 20.00           C  
HETATM    2  HAE LIG     1      -0.970   2.520   0.000  1.00 20.00           H  
HETATM    3  CAC LIG     1       0.180   0.730   0.000  1.00 20.00           C  
HETATM    4  NAA LIG     1       1.450   1.150   0.000  1.00 20.00           N  
HETATM    5  HAA LIG     1       1.750   2.100   0.000  1.00 20.00           H  
HETATM    6  CAH LIG     1       2.240   0.080   0.000  1.00 20.00           C  
HETATM    7  HAH LIG     1       3.330   0.100   0.000  1.00 20.00           H  
HETATM    8  NAB LIG     1       1.480  -1.010   0.000  1.00 20.00           N  
HETATM    9  CAD LIG     1       0.200  -0.630   0.000  1.00 20.00           C  
HETATM   10  CAF LIG     1      -0.940  -1.360   0.000  1.00 20.00           C  
HETATM   11  HAF LIG     1      -0.900  -2.450   0.000  1.00 20.00           H  
HETATM   12  CAI LIG     1      -2.180  -0.690   0.000  1.00 20.00           C  
HETATM   13  HAI LIG     1      -3.120  -1.250   0.000  1.00 20.00           H  
HETATM   14  CAG LIG     1      -2.200   0.730   0.000  1.00 20.00           C  
HETATM   15  HAG LIG     1      -3.150   1.260   0.000  1.00 20.00           H  
CONECT    1    2    3   14
CONECT    2    1
CONECT    3    1    4    9
CONECT    4    3    5    6
CONECT    5    4
CONECT    6    4    7    8
CONECT    7    6
CONECT    8    6    9
CONECT    9    3    8   10
CONECT   10    9   11   12
CONECT   11   10
CONECT   12   10   13   14
CONECT   13   12
CONECT   14    1   12   15
CONECT   15   14
END


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As I said, have a look in the documentation. You need to provide the partial charges along with your PDB file. The PDB file contains only coordinates, no chemistry.

Also, use the reply to comment feature instead of starting a new answer.

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