I have a .mol 3d structure of a nonligand molecule (piroxicam). I opened it in pymol and added hydrogens to it before saving it as .pdb file. Then I used this file as an input to ATB (http://compbio.chemistry.uq.edu.au/atb/) server to obtain the topology of piroxicam. ATB server is giving me this error -- "Your job that was submitted at 2013-07-27 03:50:06 (RNME = _PSQ) had at least one error. Specifically, the QM calculation failed. The most likely cause is that either: (1) the geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate. "
Mr. Fernandez, I am not getting your point. Can you please explain it ? When I am seeing the structure in rasmol or pymol , it looks like exactly what it should be.
Hello.
Which minimization you used? I get the same error with AM1/PM3. Only could do it using the other one.
Best regards,
Ricardo Ferreira
I think pymol and rasmol do not show bond order. Maybe you can look with another program like DSV or Avogadro. As Daniel says there may be something wrong with bonds.
I tried with all the minimizations AM1, PM3 and HF/STO-3G but was not successful. Energy minimization was successful for the "pubchem" structure. Thanks a lot.
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