Thank you for reply
I have just updated to AmberTools 15
and I am trying to replicated the tutorial that you sent me.
However I got this strange error when trying to create a box to surround
the crystal
$AMBERHOME/bin/PropPDB -p 2y3j_edited.pdb -o mol_box.pdb -X 9.560 -Y
15.640 -Z 45.230 -al 89.87 -bt 90.02 -gm 89.91
PropPDB >> Error. Unrecognized tag -X
Also is it possible not to fill the box surrounding the crystal with any
solvent and simulate periodically ?!
Regards
On Wed, Oct 14, 2015 at 4:05 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Oct 14, 2015 at 9:51 AM, Hadeer ELHabashy <
> hadeer.elhabashi.gmail.com> wrote:
>
> > Dear sir
> >
> > good day !
> >
> > I wanted to simulate a constant volume periodic box of crystal, not in
> > vacuum with igb is not 6 nor in implicit solvent with igb equal 2,5 o7
> etc
> >
> > I need to run my periodic crystal with igb=0 and ntb=1 without any kind
> of
> > solvation ,is that possible ?!
> > because every time i ran, I got the problem of " peek_ewald_inpcrd: Box
> > info not found in inpcrd"
> >
> > I need to set the dimension of this periodic box ?
> > is there any tip i should do during file preparation?
> > is there any tutorial to follow?
> >
>
> You are in luck! There is such a tutorial:
> http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html. Your
> questions should be answered in there.
>
> All of the "official" Amber tutorials are at http://ambermd.org/tutorials/
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Wed Oct 14 2015 - 11:30:06 PDT
