A comment: on the decimal place in the mol2 file format.
I have had experience with reviewers questioning the interpretation of
coordinates beyond 2nd-decimal.
Their argument was that coordinates from x-ray data are known with
certainty up to only the 2nd decimal place in Angstrom units.
Thus any v
Indeed small differences in XYZ coordinates, distances, etc. are not
meaningful, although certainly a structure can shift slightly from a true
optimum (all gradients are essentially zero) with rounding.
On the other hand, not every file format supports arbitrary precision (e.g., 8
decimals or m
If you're only sampling 20 conformers, it's unlikely to be a global minima. It
will usually be a lower energy conformer than what you started.
Does it need to be further optimized? Well, usually yes, but it depends - the
weighted search option does minimize with the MMFF94 force field by default
On 9/21/2019 11:28 AM, Geoffrey Hutchison wrote:
On the other hand, not every file format supports arbitrary precision
(e.g., 8 decimals or more) - there's not much that babel can do about
that, except by suggesting other formats with better suitability.
OTGH I've seen lots of numbers printed
