Or: I was really dumb yesterday.
I was trying to play a bit* with porphin, that being the simplest porphyrin according to Wikipedia. Being really lazy, I drew the molecule in ChemDraw, exported it as a molfile, imported that into the computation program, cleaned it a bit, then ran an optimization.
It turns out that the export (exportation?) process does not include implicit hydrogens. And I was dumb enough to not notice until this happens**:
(Yes yes I'm using GaussView/Gaussian 03W, but that's irrelevant to this discussion.)
Of course, optimizations sometimes go wrong even if the initial structure is correct. But this is just asking for trouble. So yea. Public warning. Don't be like me, and remember to check the structure for things like implicit hydrogens when importing the input file from elsewhere.
(I guess this is really only applicable when the input is exported from a drawing program like ChemDraw. It'd be unimaginably annoying to check, say, a PDB file. Also, unnecessary.)
*Y'know, instead of doing my work-related calculations like a good undergrad assistant should. But hey, it was Friday evening...
**Actually, I didn't notice the absence of hydrogens until after I restarted the calculation, and was halfway home. Of course then I have to go back and fix it.
Sunday, July 26, 2009
Easiest Troubleshooting Ever
Subscribe to:
Post Comments (Atom)
No comments:
Post a Comment