AMBER Archive (2005)

Subject: Re: AMBER: nucgen H5T H3T

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 26 2005 - 09:54:32 CDT

On Mon, Jul 25, 2005, Stern, Julie wrote:

> I've created DNA using nucgen but it appears that
> my H5T and H3T atoms aren't bound to anything? Is there
> something I'm supposed to do withing nucgen to make these
> hydrogens bind?

What is it makes you say they are not bound? They tend to be built with
slightly long bond lengths, so that a visualization program might decide
not to draw a bond between them. The "desc" command in LEaP will tell you
what the bonds are, or use can use readprm to examine the prmtop file.

....ac

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