I already have an existing model which I have to rebuild. Like you said,
there is a large gap between the loop and the rest of the structure when I
manually edited the file. This needs to be fixed.
Regards,
Sruthi Sudhakar
On Mon, Jul 19, 2021 at 7:41 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> You could use NAB to build a structure for this sequence. It isn't clear
> from your email if you have a specific structure already and want to modify
> it, or are looking to build a model. What exactly are you trying to
> achieve? If you have a PDB file, you could delete those nucleotides, but
> then there will be a very large gap between the stem and loop. You would
> need to think about how to fix that, if you try to do it in Amber you are
> likely to end up with a distorted structure. It might be easier to delete
> nucleotides from the ends and then modify the sequence of the stem to match
> what you need. We could help you do that, but are not sure what you want to
> get in the end.
>
> On Mon, Jul 19, 2021 at 7:42 AM Sruthi Sudhakar <
> sruthisudhakarraji.gmail.com> wrote:
>
> > Dear all,
> >
> > I have an RNA sequence as below:
> > 5'-GUUUUAGAGCUAUGCU*GAAA*AGCAUAGCUCUAAAAC-3'
> >
> > In this, the bold region forms a loop. I want to remove the underlined
> base
> > pairs( adjacent to the loop) and connect the loop to the rest of the
> > system. In this way my system would be shorter. Is it possible to do such
> > removal and fixing using xleap? Kindly guide regarding the same.
> > After removal my system should look like this
> >
> > 5'-GUUUUAGAGCUAU*GAAA*AUAGCUCUAAAAC-3'
> > Regards,
> > Sruthi Sudhakar
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jul 19 2021 - 08:00:02 PDT
