On Mon, Jan 25, 2010 at 12:41 PM, Antonios Samiotakis
<asamiotakis.gmail.com> wrote:
> 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.
>
Ahh this is true, I was not careful enough reading the OFF file.
Perhaps, then, you should remove all of the URE residues from your PDB
and simply solvate it in UREABOX. This should add the URE in there
for you. It is good to note, though, that if the residue does not
appear in the "list", then it will not be recognized by leap.
Is there a specific reason why using the solvate option after removing
the URE from the PDB file is not desirable? If there is a good
reason, then you should probably attempt to build an OFF file (using
saveOFF) for the URE residue.
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 - 11:30:04 PST
