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

From: David A Case <>
Date: Thu, 21 Oct 2021 16:46:13 -0600

On Thu, Oct 21, 2021, Saikat Pal wrote:
> I want to contruct a 5' protonated phosphate sequence.

In this case, you want to "loadOff terminal_monophosphate.lib" after you load
the leaprc.RNA.ROC file. This will overwrite the standard 5' nucleotide
definitions with ones that have a protonated monophosphate at the 5' end.

Then "sequence { U5 C G3 }" should get you what you want (I hope).


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Received on Thu Oct 21 2021 - 16:00:02 PDT
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