On Mon, May 9, 2011 at 8:48 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Jason
>
> I tried your suggestion. I'm copying from terminal:
>
>
> > COMPLEX=loadpdb 2wc6_bom.pdb
> Loading PDB file: ./2wc6_bom.pdb
> total atoms in file: 2256
>
> > set COMPLEX box (67.602 60.679 66.072)
>
Curly braces {}, not parentheses ()
> set: Improper number of arguments!
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
> ERROR: syntax error
>
> Cheers
>
> George
>
>
>
> On May 9, 2011, at 8:04 PM, Jason Swails wrote:
>
> > Hello,
> >
> > On Mon, May 9, 2011 at 8:00 PM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> I'm dealing with a modified trajectory file (have stripped HOHs from the
> >> original file). I need to generate a new topology file for my complex.
> >>
> >> I load my complex in tleap
> >>
> >>> COMPLEX = my_complex.pdb
> >>
> >
> > Do you mean
> >
> > COMPLEX = loadpdb my_complex.pdb
> >
> > ?
> >
> >
> >
> >>
> >> Then I try to set a unit box using the box dimensions taken from the
> >> modified trajectory file (last line).
> >>
> >> I do a
> >>
> >>> set COMPLEX box 67.602 60.679 66.072
> >>
> >> and get
> >>
> >> set: Improper number of arguments!
> >> usage: set <container> <parameter> <object>
> >> or: set default <parameter> <value>
> >>
> >
> > This means you can only have 1 value. Thus, the box dimensions must be
> an
> > array (I would guess). Try
> >
> > set COMPLEX box {67.602 60.679 66.072}
> >
> > HTH,
> > Jason
> >
> >
> >>
> >>
> >> I'd appreciate your suggestions on the correct syntax for setting the
> unit
> >> box.
> >>
> >> Many thanks in advance
> >>
> >> George
> >>
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> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 09 2011 - 12:30:02 PDT
