[AMBER] RNA - build a mismatch and a loop with NAB

From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch>
Date: Mon, 22 Oct 2012 14:11:13 +0000

Hi all, I apologise because this question is probably very silly, but I'm new to molecular modelling and to Amber, so I'm a bit (very) lost.

Can I use NAB to build a stem-loop RNA with a mistmatch in the stem? I tried giving NAB my RNA as single stranded, with the naive hope that it would just fold it. I used this:
m = fd_helix ( "arna", ...)

and ofc what NAB did was to take my sequence and build the complementary strand, to produce a perfect RNA duplex. This is not what I want...

I've tried other programs to generate a pdb with my RNA but to no availl... I've also read I can use NAB and do m=wc () instead, but I have no idea whether this will work for the loop...

Thanks very much in advance for your ideas. In you I trust! :-)
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Received on Mon Oct 22 2012 - 07:30:03 PDT
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