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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