On Mon, Jan 08, 2018, Malay Raul wrote:
> I googled this, and try to apply all the suggestions given in the site. But
> all are useless.
You won't avoid the problem, which has do to with the fact that minimization
procedure doesn't understand SHAKE constraints. Amber users generally use
minimization as a way to reduce the effects of bad interactions prior to
running MD simulations.
If you need minimization for some other purpose, you will probably need to tur
off SHAKE, and explore ntmin=3 (using the xmin minimizer). If you have a
non-periodic system, you can carry out minimization in NAB that correctly
implements the SHAKE procedure.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 07 2018 - 18:00:02 PST
