Are you sure you're using ntr and not itgtmd? The latter is the targeted md
option. Ntr=1 is for Cartesian positional restraints and no fitting is
involved.
On Thu, Jul 19, 2018, 10:57 PM 李耀 <liyao17.mails.tsinghua.edu.cn> wrote:
> Hello Amber,
>
>
> I'm using "ntr=1, restraintmask=" to run targeted MD. In the tutorial it's
> wrote that "the molecule is ’fitted’ implicitly by applying positional
> restraints to atoms specified in restraintmask". I wander in Amber if the
> these atoms (in restraintmask) of the initial structure is aligned to the
> corresponding atoms in the reference structure before running targeted MD?
> This is important for me. Thank you!
>
>
> Best,
> Yao Li
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Received on Fri Jul 20 2018 - 05:30:02 PDT
