On Wed, Jun 12, 2019, Erdem Yeler wrote:
>I realized that: tleap "impose" command isn't working for boron atoms.
>Actually, I wrote a python script and I rotated my dihedrals with this
>script but yet I wonder which elements tleap can make rotate? I read the
>amber manual but I couldn't find an answer. Can you provide an answer why I
>can not use impose command for boron atoms?
The "problem" is likely to be with the impose syntax.
Logically, to rotate about a dihedral, one needs to say "rotate this set
of atoms by this amount about this axis". The impose command asks for
the rotation amount, and specifies the axis by a pair of atoms, but
never asks which atoms should be moved; rather it tries to infer that by
looking at the topology of the system. The rules by which it makes this
inference are not well documented.
So, you'll have to either grok the code or run some experiments. It's
not clear (to me) whether the problem is that you have a boron atom, or
that tleap doesn't know what atoms are bonded to it, and can't construct
the chain. You play around (e.g. make the boron atom a phosphorus), and
learn by example how things work.
But for any non-simple/non-standard situation, many Amber users have
concluded that they can't rely on "impose", and have to write their own
codes.
We are in the (slow-ish) process of replacing tleap by entirely new
codes (
https://hub.docker.com/r/drmeister/cando/), which will have
different/better molecule building capabilities.
...dac
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Received on Wed Jun 12 2019 - 10:00:02 PDT
