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

[Maik Goette]

Sorry, but first I suggest: Read the error message!

Fatal error:
 > Residue 'UNK' not found in residue topology database

Now, what could this mean? This actually means, in the forcefield 
residue database (e.g. ffoplsaa.rtp) exists no entry for a molecule 
named UNK...
Rename the pdb to the expected name given in the rtp of the forcefield 
for your molecule, or if, more likely, the molecule really doesn't exist
you have to build an entry by either building it from reasonable 
available building blocks or parameterize it yourself...

And in general there's a very important rule to obey before posting to 
this mailinglist: RTFM...

bye

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Sagittarius wrote:
> 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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