Re: [AMBER] adding non-standard residue to RNA strand

From: David A Case <>
Date: Sat, 9 Jul 2016 18:29:41 -0400

On Sat, Jul 09, 2016, Martina Devi wrote:
> I have the given mol2 generated from RED server.I tried incorporating the
> given mol2 with the RNA strand. Though the non-standard manages to load
> through leap it does not mesh with the RNA strand.

If I am understanding you correctly, you are dealing with a modified
nucleotide that should be covalently bonded within an RNA chain. For this
purpose, you need to obtain a mol3 file from RED (not mol2). The mol3 file
has the connectivity information to tell tleap how it should be incorporated
into the RNA chain.


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Received on Sat Jul 09 2016 - 15:30:02 PDT
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