On Thu, May 18, 2017, Michael Shokhen wrote:
>
> I have AMBER16 and AMBER Tools16
>
> For atom: .R<NA 743>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
>
> tleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff14SB
You should avoid using files in the "oldff" directory. Consult the beginning
of Chap. 3 in the Reference Manual. You probably want something like this:
source leaprc.protein.ff14SB
source leaprc.water.tip3p
The leaprc.water.tip3p also automatically adds the appropraite atomic ions
set, so that you will get parameters for NA as well.
....dac
(Developers: the manual is not clear enough that loading a water leaprc
file also loads the corresponding atomic ions. It says this at the
beginning of chapter 3, and in section 3.5, but that should probably be
repeated in section 3.6 ("Ions") as well.)
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Received on Thu May 18 2017 - 07:00:05 PDT
