Well,
The idea is that I would load the UREABOX (that has 8M of urea in water) and
then solvate it with more water in order to dilute it and reduce the
concentration of urea.
Then, I would save it as prmtop and crd and equilibrate with NPT and NVT to
mix it and make it homogeneous and by doing all this I would have something
with a reduced concentration of urea in water.
Then that final equilibrated box has to be read as a pdb (I cannot convert a
restart file to anything else, that's why it has to be a pdb) , and use it
to solvate a protein or DNA etc.
Now, I can do all of the above, except for the "load the pdb part" that gets
stuck in the URE molecules.
It's funny because it seems that leap can handle the URE residues in the
8Mureabox.off file but not if I
attempt to load them in the form of pdb.
I think the best way is probably to save an off file of the box right after
I dilute it, since leap has no problem in reading off files
with urea.
Then after, it's equilibrated I can change the coordinates in the .off file
with the new ones, and then read this on leap and use it to solvate a
protein.
I was just wondering if anyone had encountered this problem before and how
was it dealt...
Thanks anyway for the help...
Antonios
On Mon, Jan 25, 2010 at 1:16 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
--
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 - 12:30:02 PST
