Thanks a lot!
I've try to use another conformation and it worked even without modifing
the leaprc file.
Now I'm stuck again but with a different protein and with different
residues. Apparently seems like the hydrogens could be a problem, so I used
the comands:
reduce -build
and
reduce -trim
With the first command you add hydrogens while with the second you remove
all of them and then let leap to the job of applying them back right?
After that, I went back to leap, loaded the molecule and applied the check
command.
Thanks in advance
Regards,
Mahad
2015-01-30 16:48 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
> On Fri, 2015-01-30 at 16:33 +0100, Mahad Gatti Iou wrote:
> > Thanks a lot.
> >
> > I was able to obtain the .prmtop and .inpcrd finally.
> > So, I presume that deleting this line avoids to have a U5 residue as a 5'
> > terminal and a U3 residue as a 3' terminal, any other atom is accepted as
> > terminal right?
>
> Atoms are not terminal -- residues are. A non-terminal residue is one
> that has a dangling valence on both ends, expecting to be bound to the
> residues adjacent to it.
>
> > If that so does this makes sense? For the purpose of simulating RNA, it
> is
> > necessary to leave the terminal to achieve better results or even like
> this
> > is still acceptable?
>
> I'm not exactly sure what you did, but it *seems* that all you did was
> delete the line in the leaprc file that assigns a chain-ending RU to be
> RU5. If this is indeed what you did, look at your structure in VMD, and
> run the "netCharge" command in ParmEd, and you will see that you have a
> PO2 group and a non-integer charge (the 3' and 5' residues each have a
> non-integral charge that adds to an integer, which means you need both
> termini to get a physically realistic charge).
>
> So I'm not sure if this is OK for your model, but my guess would be "not
> really".
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Feb 05 2015 - 09:00:03 PST
