Dear researchers,
I tried to obtain a topology file of a compound with PubChem CID of 134149698 from swissparam. Following is the error message.
Please let me know the way to solve it.
Thanking you.
------------ERROR----------- Thank you for using SwissParam. Unfortunately, topology and parameters were not successfully generated for LIG. A failure report can be found below.
Failure report:
It was necessary to change the name of the atoms numbered : 5 ( N -> N1 ) 6 ( N -> N2 ) 7 ( N -> N3 ) 9 ( C -> C1 ) 10 ( C -> C2 ) 11 ( C -> C3 ) 12 ( C -> C4 ) 13 ( C -> C5 ) 14 ( C -> C6 ) 15 ( C -> C7 ) 16 ( C -> C8 ) 17 ( C -> C9 ) 18 ( C -> C10 ) 19 ( C -> C11 ) 20 ( C -> C12 ) 21 ( C -> C13 ) 22 ( C -> C14 ) 23 ( C -> C15 ) 25 ( H -> H1 ) 26 ( H -> H2 ) 27 ( H -> H3 ) 28 ( H -> H4 ) 29 ( H -> H5 ) 30 ( H -> H6 ) 31 ( H -> H7 ) 32 ( H -> H8 ) 33 ( H -> H9 ) 34 ( H -> H10 ) 35 ( H -> H11 ) 36 ( H -> H12 ) 37 ( H -> H13 ) 38 ( H -> H14 ) Possible problem with molecular topology in LIG.mol2. SwissParam will try to reconstruct the topology from coordinates only. Topology and parameters were NOT generated. Please check the validity of your molecule. - Are all hydrogens present in the mol2 file? - Is the mol2 file correct? Please, read "How to obtain a correct mol2 file?" in the www.swissparam.ch website.
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