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Dear users<br>
<br>
I would like to perform a MD simulation of Sedoheptulose (C<sub>7</sub>H<sub>14</sub>O<sub>7</sub>)
via Gromacs. But already during pdb2gmx it comes up with:<br>
"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?<br>
<br>
the sedoheptulose data to start from is:<br>
ATOM 1 C UNK 0 -3.442 2.742 0.000 0.00
0.00 C+0<br>
ATOM 2 C UNK 0 -2.108 3.512 0.000 0.00
0.00 C+0<br>
ATOM 3 C UNK 0 -0.774 2.742 0.000 0.00
0.00 C+0<br>
ATOM 4 C UNK 0 0.559 3.512 0.000 0.00
0.00 C+0<br>
ATOM 5 C UNK 0 1.893 2.742 0.000 0.00
0.00 C+0<br>
ATOM 6 C UNK 0 3.227 3.512 0.000 0.00
0.00 C+0<br>
ATOM 7 O UNK 0 -0.774 1.202 0.000 0.00
0.00 O+0<br>
ATOM 8 O UNK 0 0.559 5.052 0.000 0.00
0.00 O+0<br>
ATOM 9 O UNK 0 1.893 1.202 0.000 0.00
0.00 O+0<br>
ATOM 10 O UNK 0 -4.775 3.512 0.000 0.00
0.00 O+0<br>
ATOM 11 O UNK 0 -2.108 5.052 0.000 0.00
0.00 O+0<br>
ATOM 12 H UNK 0 -6.109 2.742 0.000 0.00
0.00 H+0<br>
ATOM 13 H UNK 0 -0.774 5.822 0.000 0.00
0.00 H+0<br>
ATOM 14 H UNK 0 1.893 5.822 0.000 0.00
0.00 H+0<br>
ATOM 15 H UNK 0 0.559 0.432 0.000 0.00
0.00 H+0<br>
ATOM 16 H UNK 0 3.227 0.432 0.000 0.00
0.00 H+0<br>
ATOM 17 C UNK 0 4.560 2.742 0.000 0.00
0.00 C+0<br>
ATOM 18 O UNK 0 5.894 3.512 0.000 0.00
0.00 O+0<br>
ATOM 19 H UNK 0 7.228 2.742 0.000 0.00
0.00 H+0<br>
ATOM 20 O UNK 0 3.227 5.052 0.000 0.00
0.00 O+0<br>
<br>
cheers<br>
bernhard<br>
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