[gmx-users] pdb does not work.

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 16 05:48:03 CEST 2009


Joseph Johnson wrote:
> Just as a test run I wanted to see if I could simulate 5 repeats of 
> glycine.  I give the command:
> 
> pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro
> 
> and I tell it to do:
> 
> 0: GROMOS96 43a1 force field
> 
> The output I get is:
> 
> Program pdb2gmx, VERSION 3.3.1
> Source code file: resall.c, line: 438
> 
> Fatal error:
> Residue '1' not found in residue topology database
> 
> Why is it giving me this output?  Here is my pdb file and thank you for 
> your help :)

... because your PDB file does not name your residues. pdb2gmx isn't 
magic - it depends on the residue name to recognize which entry in the 
residue topology database (.rtp file) should be applied. So, read the 
PDB format document to work out which columns should have "GLY", or use 
a known-good PDB file to copy the right columns.

Mark

> HETATM    1  C           1      -3.361   1.127   
> 2.911                       C
> HETATM    2  H           1       0.919   3.113   
> 3.939                       H
> HETATM    3  H           1      -0.857   0.007   
> 3.031                       H
> HETATM    4  H           1      -3.184   0.097   
> 4.698                       H
> HETATM    5  H           1      -5.242   0.080   
> 2.911                       H
> HETATM    6  O           1      -4.328   0.360   
> 0.373                       O
> HETATM    7  H           1      -5.934   2.635   
> 1.818                       H
> HETATM    8  H           1      -6.637   2.054  
> -0.750                       H
> HETATM    9  H           1      -4.459   1.860  
> -2.600                       H
> HETATM   10  H           1      -5.242  -0.129  
> -4.291                       H
> HETATM   11  C           1      -5.524   2.053  
> -0.750                       C
> HETATM   12  H           1      -4.698  -2.790  
> -3.382                       H
> HETATM   13  H           1      -6.834  -4.217  
> -4.291                       H
> HETATM   14  H           1      -9.153  -2.809  
> -3.382                       H
> HETATM   15  H           1      -9.153  -4.576  
> -3.382                       H
> HETATM   16  H           1      -3.758  -0.655  
> -3.381                       H
> HETATM   17  O           1      -1.506   2.874   
> 3.937                       O
> HETATM   18  O           1       0.594   2.197   
> 3.939                       O
> HETATM   19  H           1      -0.858   0.009   
> 4.849                       H
> HETATM   20  C           1      -0.722   1.955   
> 3.939                       C
> HETATM   21  N           1      -5.355  -2.021  
> -3.382                       N
> HETATM   22  C           1      -1.227   0.533   
> 3.939                       C
> HETATM   23  N           1      -2.677   0.534   
> 3.939                       N
> HETATM   24  O           1      -2.756   1.649   
> 2.005                       O
> HETATM   25  H           1      -5.240   1.655   
> 3.818                       H
> HETATM   26  C           1      -4.870   1.129   
> 2.910                       C
> HETATM   27  N           1      -5.352   1.811   
> 1.725                       N
> HETATM   28  H           1      -5.152   3.102  
> -0.751                       H
> HETATM   29  C           1      -5.022   1.342   
> 0.483                       C
> HETATM   30  N           1      -5.042   1.369  
> -1.934                       N
> HETATM   31  O           1      -6.068  -0.528  
> -1.354                       O
> HETATM   32  C           1      -5.373   0.058  
> -2.150                       C
> HETATM   33  C           1      -4.871  -0.654  
> -3.382                       C
> HETATM   34  O           1      -7.486  -1.352  
> -3.382                       O
> HETATM   35  H           1      -6.834  -4.217  
> -2.473                       H
> HETATM   36  C           1      -7.205  -3.693  
> -3.382                       C
> HETATM   37  N           1      -8.643  -3.693  
> -3.382                       N
> HETATM   38  C           1      -6.701  -2.270  
> -3.382                       C
> CONECT    1   24   23   26
> CONECT    2   18
> CONECT    3   22
> CONECT    4   23
> CONECT    5   26
> CONECT    6   29
> CONECT    7   27
> CONECT    8   11
> CONECT    9   30
> CONECT   10   33
> CONECT   11    8   28   29   30
> CONECT   12   21
> CONECT   13   36
> CONECT   14   37
> CONECT   15   37
> CONECT   16   33
> CONECT   17   20
> CONECT   18    2   20
> CONECT   19   22
> CONECT   20   17   18   22
> CONECT   21   12   33   38
> CONECT   22    3   19   20   23
> CONECT   23    4   22    1
> CONECT   24    1
> CONECT   25   26
> CONECT   26    5   25    1   27
> CONECT   27    7   26   29
> CONECT   28   11
> CONECT   29    6   27   11
> CONECT   30    9   11   32
> CONECT   31   32
> CONECT   32   31   30   33
> CONECT   33   10   16   32   21
> CONECT   34   38
> CONECT   35   36
> CONECT   36   13   37   38   35
> CONECT   37   14   15   36
> CONECT   38   34   21   36
> END
> 
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