AMBER Archive (2004)

Subject: AMBER: RNA sequence with DNA backbone?

From: Arvind (arvind_at_mbu.iisc.ernet.in)
Date: Mon Jul 12 2004 - 06:26:36 CDT

Hi all,
i am planning to do a MD simulation of a nucgen generated dodecamer
CGCAAAUUUGCG but with a DNA backbone. Is this possible in AMBER?

I tried 2 ways, both of which failed:
1) I generated a DNA dodecamer with 'T' instead of 'U' and deleted C7 from
each T. But leap adds the C7 once again.

2) I generated a RNA dodecamer and deleted the backbone O2' but again it
was added as a missing heavy atom by leap.

Can anyone suggest a way around this difficulty? Thanx in advance. 

-- 
Regards,
Arvind.

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