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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Received on Mon Jan 25 2010 - 09:30:03 PST
