Thank you Jason for your reply,
I have already loaded the 8Mureabox.off in my leaprc file.
However, even if 8Mureabox is loaded, URE is not on the list,
just UREABOX.
On Mon, Jan 25, 2010 at 11:16 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Mon, Jan 25, 2010 at 12:06 PM, Antonios Samiotakis
> <asamiotakis.gmail.com> wrote:
> > Hi AMBER users and developers,
> >
> > I am trying to edit the UREABOX unit, in order to reduce the urea
> > concentration from 8M, to
> > lower values.
> >
> > I am following this procedure suggested by Ross Walker:
> >
> > http://archive.ambermd.org/200804/0315.html
> >
> > The problem I am having is that after I equilibrate the new urea box,
> > xleap does not recognize the URE residues when I attempt to load the pdb.
>
> Have you loaded the 8Mureabox.off library file in leap? If you have
> not loaded this file by hand, then it will certainly not recognize
> your URE residue names.
>
> Use the command "loadoff 8Mureabox.off" in leap to load the URE
> residue into leap. You can always use the "list" command to have leap
> list the residues, units, etc. that leap is aware of. If you do not
> see URE there, then it will not recognize those residues in PDB files.
>
> Good luck!
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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>
--
Antonios Samiotakis
Department of Physics
University of Houston
4800 Calhoun Rd
SR1 Rm 629G, Houston
TX, 77204
e-mail: asamiotakis2_at_uh.edu
http://www.phys.uh.edu/~mscheung/antonios.htm
Tel: 713-743-3725
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Received on Mon Jan 25 2010 - 10:00:03 PST
