I have solved this situation by adding the CRYST card to the PDB and only
used
$AMBERHOME/bin/PropPDB -p 2y3j_edited.pdb -o mol_box.pdb -ix 2 -iy 2 -iz
2
On Wed, Oct 14, 2015 at 8:23 PM, Hadeer ELHabashy <
hadeer.elhabashi.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Oct 14 2015 - 12:00:05 PDT
