Omega2 failing due to missing parameters
I am trying to generate an ensemble of conformers for the anti HIV drug zidovudine, but when running OMEGA2, the calculatio fails due to missing parameters (in the force field?) for the specified molecule. The output in the .log file is as follows:
OMEGA started on host Fredy-PC
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Title = [C][c]1[c][n]([c](=O)[n][c]1=O)[C]2[C][C]([C]([C][O])[O]2)[N]=N#N
Warning: force field setup failed due to missing parameters for molecule [C][c]1[c][n]([c](=O)[n][c]1=O)[C]2[C][C]([C]([C][O])[O]2)[N]=N#N
Is there any why in which the missing parameters can be included in the calculation?
Thanks in advance for the support,
Best regards
Alfredo
Thank you very much James for the answer. Your explanation was very clear and solved the problem.
Kind regards
Alfredo
Alfredo
Omega does have a 3 flags relating to strictness, -strictstereo, -strictatomtyping, and -strictfrags. -strictstereo and -strictatomtyping are true by default. This means that Omega expects stereo to be defined for each stereocenter and for there to be no unknown atom types. Setting 'false' for these flags will result in Omega choosing stereo and trying to substitute a known atom type for an unknown one.
However for this molecule Omega cannot build a 3D structure as the molecule is simply too badly defined. When you see [C] or [n] in a SMILES string this should always be a warning that the molecule is not correct, the square brackets indicates that the hydrogen count for the molecule is incorrect. I don't know what format you are using for the input to Omega but some formats are worse than others. E.g .xyz contains no bond or atom type information. Small ligands from the PDB can also be poor.
The correct SMILES for zidovudine is Cc1cn(c(=O)[nH]c1=O)[C@H]2C[C@@H]([C@H](O2)CO)N=[N+]=[N-] If you use this as input to Omega you will get conformers built.
I hope this is useful
P.S. We are transferring all forums and such to a new site http://hivemind.eyesopen.com/ That is now the recommended venue for asking questions.