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 Fri Jan 30 2015 - 08:00:06 PST
