[gmx-users] pdb2gmx fatal error

[Ali Khodayari]

Dear gmx users,

 

I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names
were modified according to the rtp file of the force field. Yet, I get the
following error while I perform pdb2gmx command:

 

Fatal error:

Residue 4 named GLC of a molecule in the input file was mapped to an entry
in the topology database, but the atom C6 used in that entry is not found in
the input file. Perhaps your atom and/or residue naming needs to be fixed."

 

I also tried to delete the hydrogens in the pdb file but the error changed
to the following:

 

Fatal error:

Residue 876814369 named GLC of a molecule in the input file was mapped to an
entry in the topology database, but the atom C3 used in an interaction of
type improper in that entry is not found in the input file. Perhaps your
atom and/or residue naming needs to be fixed.

 

Ignoring the hydrogens through -ignh will give the first error as well.
Then I added the GLC residue to the residuetypes.dat and the error changed
to:

 

Fatal error:

atom N not found in buiding block 1GLC while combining tdb and rtp

 

Is there anything wrong with the pdb file? Here is the entry of it:

 

ATOM      1  C1  GLC     2    3.992   3.199    3.177  1.00  0.04
C    

ATOM      2  C2  GLC     2    3.597   2.204    2.072  1.00  0.04
C    

ATOM      3  C3  GLC     2    4.231   2.633    0.737  1.00  0.04
C    

ATOM      4  C4  GLC     2    3.713   4.036    0.378  1.00  0.04
C    

ATOM      5  C5  GLC     2    4.096   5.017    1.502  1.00  0.04
C    

ATOM      6  C6  GLC     2    3.581   6.419    1.132  1.00  0.04
C    

ATOM      7  O2  GLC     2    4.094   0.828    2.442  1.00  0.04
O    

ATOM      8  O5  GLC     2    3.476   4.569    2.805  1.00  0.04
O    

ATOM      9  O6  GLC     2    4.207   6.834   -0.178  1.00  0.04
O    

ATOM     10  H1  GLC     2    5.128   3.219    3.268  1.00  0.00
H    

ATOM     11  H2  GLC     2    2.462   2.181    1.967  1.00  0.00
H    

ATOM     12  H3  GLC     2    5.366   2.661    0.847  1.00  0.00
H    

ATOM     13  H4  GLC     2    2.578   4.005    0.271  1.00  0.00
H    

ATOM     14  H5  GLC     2    5.230   5.045    1.611  1.00  0.00
H    

ATOM     15  H61 GLC     2    3.858   7.165    1.950  1.00  0.00
H    

ATOM     16  H62 GLC     2    2.449   6.385    1.015  1.00  0.00
H    

ATOM     17  HO2 GLC     2    5.198   0.853    2.551  1.00  0.00
H    

ATOM     18  HO6 GLC     2    5.313   6.850   -0.083  1.00  0.00
H    

ATOM     19  O1  GLC     3    4.312   4.595    9.824  1.00  0.04
O  

ATOM     20  C1  GLC     3    3.708   4.145    8.515  1.00  0.04
C    

ATOM     21  C2  GLC     3    4.109   5.126    7.399  1.00  0.04
C    

ATOM     22  C3  GLC     3    3.497   4.668    6.062  1.00  0.04
C    

ATOM     23  C4  GLC     3    4.005   3.250    5.730  1.00  0.04
C    

ATOM     24  C5  GLC     3    3.616   2.295    6.877  1.00  0.04
C    

ATOM     25  C6  GLC     3    4.151   0.877    6.596  1.00  0.04
C    

ATOM     26  O2  GLC     3    3.601   6.506    7.743  1.00  0.04
O    

ATOM     27  O3  GLC     3    3.909   5.661    5.002  1.00  0.04
O    

ATOM     28  O1  GLC     2    3.396   2.685    4.467  1.00  0.04
O    

ATOM     29  O5  GLC     3    4.225   2.770    8.173  1.00  0.04
O    

ATOM     30  O6  GLC     3    3.558   0.309    5.328  1.00  0.04
O    

ATOM     31  H1  GLC     3    2.572   4.115    8.609  1.00  0.00
H    

ATOM     32  H2  GLC     3    5.244   5.151    7.307  1.00  0.00
H    

ATOM     33  H3  GLC     3    2.361   4.651    6.153  1.00  0.00
H    

ATOM     34  H4  GLC     3    5.141   3.258    5.636  1.00  0.00
H    

ATOM     35  H5  GLC     3    2.480   2.262    6.979  1.00  0.00
H    

ATOM     36  H61 GLC     3    3.879   0.196    7.468  1.00  0.00
H    

ATOM     37  H62 GLC     3    5.286   0.920    6.494  1.00  0.00
H    

ATOM     38  HO2 GLC     3    2.496   6.480    7.836  1.00  0.00
H    

ATOM     39  HO3 GLC     3    5.015   5.674    4.919  1.00  0.00
H    

ATOM     40  HO6 GLC     3    2.453   0.270    5.418  1.00  0.00
H    

ATOM     41  O3  GLC     2    3.852   1.653   -0.348  1.00  0.00
O    

ATOM     42  HO3 GLC     2    4.305   1.969   -1.311  1.00  0.00
H    

TER      43 

END

 

P.S.: The file is well written and doesn't look like the one above, as far
as the column arrangement is concerned.

 

Regards,

Ali