Re: [AMBER] Structure alteration and shortening of loops using xleap

From: Carlos Simmerling <>
Date: Mon, 19 Jul 2021 10:10:51 -0400

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 <> wrote:

> Dear all,
> I have an RNA sequence as below:
> 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
> Regards,
> Sruthi Sudhakar
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Received on Mon Jul 19 2021 - 07:30:02 PDT
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