AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Wed Dec 27 2006 - 13:42:42 CST

"set RA.1 connect0 RA.1.P" seems to work OK, leap gives no reply and the head of
each residue is joined by the P correctly. "set RA.1 connect1 RA.1.O2*" and
leap replies with:

set: Improper number of arguments!
usage: set <container> <parameter> <object>
   or: set default <parameter> <value>

I looked at the .off file and can't make much sense of it.

Thanks,
SETH

Quoting "David A. Case" <case_at_scripps.edu>:

> On Wed, Dec 27, 2006, Seth Lilavivat wrote:
>
> > I tried setting the tail, head, connect1, and connect0 with no result :(
>
> Not sure what you mean by "no result" here. Did LEaP give any reply? Try
> using saveOff to save your residue, then examine (and perhaps modify) the
> connect0 and connect1 atoms.
>
> ...regards...dac
>
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