Hi,
Amber16 modified the way parameters are sourced by leap - now you will need
to explicitly source a leaprc file with the water model you want to use.
If you add:
source leaprc.water.tip3p
below where you source your force field leaprc, this input should work.
Check out Pengfei's leap tutorial to get a better idea of what's going on:
http://ambermd.org/tutorials/pengfei/
Hope this helps,
Christina
On Tue, Sep 27, 2016 at 8:53 AM, windy <chxp_moon.163.com> wrote:
> Hi, Everyone
>
> Recently, I using amber16 update13 to run my md. However I cannot
> generate the right prmtop by using following scripts:
>
> source leaprc.protein.ff03.r1
> REC = sequence {ACE ALA NME}
> savepdb REC ala.pdb
> solvateoct REC TIP3PBOX 12.0 1.0
> saveamberparm REC ala.prmtop ala.inpcrd
> quit
>
> The important error is here:
> solvateOct: Argument #2 is type String must be of type: [unit]
> usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
>
> However the script is works well under Amber12. What happend to the new
> tleap? Anyone have ideas?
>
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
---------------------------------------------------------------------------------------
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Received on Tue Sep 27 2016 - 06:30:02 PDT
