[gmx-users] sedoheptulose

[Bernhard Knapp]

Dear users

I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via 
Gromacs. But already during pdb2gmx it comes up with:
"Residue 'UNK' not found in residue topology database" which is 
obviously clear since sedoheptulose is not an amino acid. Is it somehow 
possible to simulate this molecule?

the sedoheptulose data to start from is:
ATOM      1  C   UNK     0      -3.442   2.742   0.000  0.00  
0.00           C+0
ATOM      2  C   UNK     0      -2.108   3.512   0.000  0.00  
0.00           C+0
ATOM      3  C   UNK     0      -0.774   2.742   0.000  0.00  
0.00           C+0
ATOM      4  C   UNK     0       0.559   3.512   0.000  0.00  
0.00           C+0
ATOM      5  C   UNK     0       1.893   2.742   0.000  0.00  
0.00           C+0
ATOM      6  C   UNK     0       3.227   3.512   0.000  0.00  
0.00           C+0
ATOM      7  O   UNK     0      -0.774   1.202   0.000  0.00  
0.00           O+0
ATOM      8  O   UNK     0       0.559   5.052   0.000  0.00  
0.00           O+0
ATOM      9  O   UNK     0       1.893   1.202   0.000  0.00  
0.00           O+0
ATOM     10  O   UNK     0      -4.775   3.512   0.000  0.00  
0.00           O+0
ATOM     11  O   UNK     0      -2.108   5.052   0.000  0.00  
0.00           O+0
ATOM     12  H   UNK     0      -6.109   2.742   0.000  0.00  
0.00           H+0
ATOM     13  H   UNK     0      -0.774   5.822   0.000  0.00  
0.00           H+0
ATOM     14  H   UNK     0       1.893   5.822   0.000  0.00  
0.00           H+0
ATOM     15  H   UNK     0       0.559   0.432   0.000  0.00  
0.00           H+0
ATOM     16  H   UNK     0       3.227   0.432   0.000  0.00  
0.00           H+0
ATOM     17  C   UNK     0       4.560   2.742   0.000  0.00  
0.00           C+0
ATOM     18  O   UNK     0       5.894   3.512   0.000  0.00  
0.00           O+0
ATOM     19  H   UNK     0       7.228   2.742   0.000  0.00  
0.00           H+0
ATOM     20  O   UNK     0       3.227   5.052   0.000  0.00  
0.00           O+0

cheers
bernhard

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