[gmx-users] Residue 'UNK' not found in residue topology database

Sagittarius deckuofm at yahoo.com
Thu Aug 16 17:33:23 CEST 2007


Dear Gromacs users,
   
  Could you please help me to find out what the problem is.
I use command

  pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top
   
  formaldehyde.pdb looks like this:

  COMPND    UNNAMED                                                     
REMARK   1 PDB to MMOD atom-numbering translation table; the mmod numbers
REMARK   1 pertain to the .dat file from which this file was created,
REMARK   1 not to one created from this file:
REMARK   1  PDB:     1     2     3     4  
REMARK   1 MMOD:     1     2     3     4 /
HETATM    1  C01 UNK     0       0.000   0.302   0.000  0.00  0.00   0
HETATM    2  O02 UNK     0       0.000   1.510   0.000  0.00  0.00   0
HETATM    3  H03 UNK     0      -0.960  -0.262   0.000  0.00  0.00   0
HETATM    4  H04 UNK     0       0.960  -0.262   0.000  0.00  0.00   0
CONECT    1    3    4
CONECT    1    2
CONECT    1    2
CONECT    2    1
CONECT    2    1
CONECT    3    1
CONECT    4    1
END
   
  Gromacs output is
  -------------------------------------------------------
Program pdb2gmx, VERSION 
Source code file: C:\Program Files\Microsoft Visual Studio\MyProjects\pdb2gmx\pdb2gmx\resall.cpp, line: 493
  Fatal error:
Residue 'UNK' not found in residue topology database
  -------------------------------------------------------
  Thanx for Using GROMACS - Have a Nice Day
   
  Thank you in advance
   

       
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