Although, I m getting results with Autodock 4.2, but further, to strengthen my results I am trying to use Swissdock, but every time the website reported the topology of ligand is not correct. Till now I have tried many ways to draw and optimized my ligands but its still not working. Can anyone help me to solve this issue.
Hi Arpana,
Maybe the .mol2 file that swissdock requires contains errors. You can choose to create this file with PRODRG server or Avogadro.
Thanks Martiniano Bello. I used swissparam and got following error
hank you for using SwissParam.
Unfortunately, topology and parameters were not successfully generated for Cp6-1. A failure report can be found below.
Failure report:
It was necessary to change the name of the atoms numbered : 2 ( O -> O1 ) 3 ( O -> O2 ) 4 ( O -> O3 ) 5 ( O -> O4 ) 6 ( O -> O5 ) 8 ( N -> N1 ) 9 ( N -> N2 ) 10 ( N -> N3 ) 12 ( C -> C1 ) 13 ( C -> C2 ) 14 ( C -> C3 ) 15 ( C -> C4 ) 16 ( C -> C5 )
Hello Arpana Parihar
Perhaps you can edit the atoms number using notepad?
Otherwise, do share your ligand file in pdb format here and I (or anyone else) can try to convert it into a proper mol2 file
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