Sounds like something for the VMD mailing list...
Marc
On 10 May 2012 07:31, "Albert" <mailmd2011.gmail.com> wrote:
> hello guys:
>
> thank you very much for kind advices. here is what I did:
>
> setBox mol vdw
>
> set mol box { 59.566 59.566 96.412 }
>
> when I load it into VMD by command:
>
> vmd apo.prmtop -rst7 apo.inpcrd
>
> I get information:
>
> Box Dimensions are 59.566002 59.566002 96.412003 90.000000
> 90.000000 90.000000
>
> However, when I type command in vmd : pbc box
>
> it said:
>
> -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
> Have you forgotten to set the pbc parameters?
>
> I am just wondering why it doesn't display the pbc box?
>
> thank you very much
> Albert
>
> On 05/09/2012 10:36 PM, Bill Ross wrote:
> > usage: setBox<unit> vdw|centers [ clearance |<clearance_xyz_list> ]
> >
> > As I remember it, setBox takes the unit and, without reorienting
> > it, uses either vdw boundaries or atom centers to draw a box with
> > an optional clearance in all directions or an optional list of
> > clearances in the x,y,z directions. If the box is already equilibrated,
> > the vdw option would introduce voids at the edges which would take
> > more equilibration than otherwise, but since the system needs to be
> > warmed up anyway, this is probably not a factor.
> >
> > Bill
> >
> > Albert<mailmd2011.gmail.com> wrote:
> >
> >> Hello Jason:
> >> thank you very much for your kind helps.
> >> I generate the system from CHARMM GUI and it contains solvent, ions
> >> and protein for a full MD system, then I import it into tleap to
> >> generate Amber input file. I've obtained the periodic information such
> as:
> >>
> >> CRYST1 59.566 59.566 96.412 90.00 90.00 90.00 P 1 1
> >>
> >> I don't find detailed comments for this 'setBox' in the manual or online
> >> tutorial expect helps from tleap:
> >>
> >> usage: setBox<unit> vdw|centers [ clearance |<clearance_xyz_list> ]
> >>
> >> do you have any idea how should I use this command correctly? Probably
> >> like the following?
> >>
> >> setBox 0 0 0 59.566 59.566 96.412
> >>
> >>
> >>
> >>
> >> On 05/09/2012 09:41 PM, Jason Swails wrote:
> >>> You can use the "setBox" command in tleap to add periodic box
> information.
> >>> If you add a solvent box, this should be done automatically.
> >>>
> >>> HTH,
> >>> Jason
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>
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Received on Thu May 10 2012 - 01:00:02 PDT
