[gmx-users] UNK not found

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:
> The following is a part of a .pdb file I generated.
> 
> 
> HETATM  250  C1  UNK     1      18.454  11.417  22.519  1.00  0.00        
>   C
> HETATM  251  C2  UNK     1      19.297  10.247  22.595  1.00  0.00        
>   C
> HETATM  252  C3  UNK     1      19.949   9.511  21.410  1.00  0.00        
>   C
> HETATM  253  C4  UNK     1      20.244   8.034  21.669  1.00  0.00        
>   C
> HETATM  254  C5  UNK     1      21.458   7.527  21.887  1.00  0.00        
>   C
> HETATM  255  C6  UNK     1      22.793   8.230  22.144  1.00  0.00        
>   C
> HETATM  256  C7  UNK    1      22.749   9.752  22.264  1.00  0.00           C
> HETATM  257  C8  UNK     1      23.873  10.420  23.098  1.00  0.00        
>   C
> HETATM  258  H1  UNK     1      22.039   6.693  21.885  1.00  0.00        
>   H
> HETATM  259  H2  UNK     1      19.416   7.379  21.609  1.00  0.00        
>   H
> 
> ... etc.
> 
> I'm getting an UNK not found in residue topology error message.
> After I run
> pdb2gmx -f XXX.pdb -o conf.pdb
> 
> Fatal error:
> Residue 'UNK' not found in residue topology database
> 
> I tried replacing UNK with H and C, respectively, and still got the same
> error except with "Residue 'H' not...".
> 
> What do I replace the UNK with to run the file smoothly or how do I add
> the unknown atom types so that the command runs?
> 

Please make use of the list archive and Gromacs website.  This error, in many 
forms, has been asked and answered a thousand times over.  Moreover:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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