Hi Jason,
Thank you for making that file for me.
Loading the urea.off you sent me and then reading a pdb in leap with URE
residues works fine now.
Thanks again for all your help.
Antonios
On Mon, Jan 25, 2010 at 3:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Mon, Jan 25, 2010 at 3:11 PM, Antonios Samiotakis
> <asamiotakis.gmail.com> wrote:
> > 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 think that the easiest way would probably be to make a "urea.off"
> file that has the unit URE in it. That way, leap would recognize it.
> It's a fairly simple process, so I created a file urea.off and used
> the charges defined in 8Mureabox.off for the urea molecules as the
> charges.
>
> I've attached the off file that I created. Try loading this library
> file ("loadoff urea.off") and trying again.
>
> However, keep in mind that all a lib file does is store a layout of
> the residue (so that it can fill in missing atoms according to the
> template) and the charges. You'll still have to load the force field
> parameters (frcmod.ureabox in addition to leaprc.ff99SB if that's the
> force field you're using)
>
> 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 - 15:30:03 PST
