lindahl at stanford.edu
Tue Nov 12 19:40:51 CET 2002
You may not like this, but especially for a small molecules that are
> non-standard you have to check manually whether the toplogy makes
> This is your research and you have to be able to explain why you have
> used such and such parameters.
This cannot be stressed enough.
There are programs like Macromodel/batchmin that try to perform an
automatic assignment of parameters. Unfortunately, my experience is
that there are very often
errors in these assignments, even when Macromodel claims it is only
using "high quality parameters".
The last time I checked a Macromodel topology the program didn't even
check that the system was neutral, but it had chosen parameters that
gave a charge of +0.6 for a ~30 atom hydrocarbon.
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