Dear AMBER Users and Experts,
I am trying to perform a simulation of a small molecule that was built
using the corresponding SMILES string. Here is what is look like (top):
HETATM 1 C1 UNK A 1 -1.519 5.742 -9.320 1.00 0.00
C
HETATM 2 C2 UNK A 1 -2.009 5.017 -8.101 1.00 0.00
C
HETATM 3 C3 UNK A 1 -1.017 5.183 -6.988 1.00 0.00
C
HETATM 4 C4 UNK A 1 -1.507 4.458 -5.770 1.00 0.00
C
HETATM 5 C5 UNK A 1 -0.515 4.624 -4.657 1.00 0.00
C
HETATM 6 C6 UNK A 1 -1.005 3.899 -3.438 1.00 0.00
C
HETATM 7 C7 UNK A 1 -0.014 4.066 -2.325 1.00 0.00
C
HETATM 8 C8 UNK A 1 -0.503 3.340 -1.107 1.00 0.00
C
.................................................
How do I go about dealing with residue type 'UNK' and preparing the
corresponding AMBER topology files to perform an MD run?
Any help would be appreciated.
Sincerely,
PN
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Received on Tue Nov 14 2023 - 14:00:03 PST
