Re: [AMBER] Query regarding not integral charge in RNA

From: David A Case <>
Date: Thu, 21 Oct 2021 12:17:23 -0600

On Thu, Oct 21, 2021, Saikat Pal wrote:

>I have generated a RNA sequence in tleap using the following command:source
>m = sequence {OHE U C G}

What you wnat here is sequence { U5 C G3 }. This will "cap" the 5' and 3'
ends of the sequence in the intended way. Try that, and see if you get what
you want.

[Aside 1: when reading PDB files, tleap by default makes the first
nucleotide a 5' version, and the final nucleotide is made a 3' variant. But
this default doesn't persist into the "sequence" command: there you have to
specify the "5" and "3" labels specifically.]

[Aside 2: the three-dimensional structure you will get by just using a
sequence command may not be what you want. A general alternative is to use
a different program to create a three-dimensional structure, and then just
read that into tleap. (Amber's NAB is one such program, but probably not
the best one for most people today.) Remember that tleap is a very "dumb"
program -- it primarily does bookkeeping. Don't expect it to actually know
anything about RNA.]


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Received on Thu Oct 21 2021 - 11:30:02 PDT
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