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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- application/octet-stream attachment: urea.off
Received on Mon Jan 25 2010 - 15:00:02 PST
