AMBER Archive (2005)

Subject: RE: AMBER: Leap set head/tail question

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Aug 03 2005 - 16:40:23 CDT

Dear Kara,

As explained by Ross, you use either

set DG head DG.1.P

or

set DG head DG.1.1

if 'P' has the atom number '1'. The reason why this is useful is, because
sometimes you might have an atom name 'O3*', and when it is the 'tail'
part, it will not accept 'set DG tail DG.1.O3*'. So, using the atom number
works, too. You can check the head and tail atoms of your residue by
'check <RESNAME>'.

Best,

On Tue, 2 Aug 2005, Ross Walker wrote:

> Dear Kara,
>
> > " followed by the atom. How do I specify the atom. When I
> > type in P,
> > it get a message "must be of type atom". The manual doesn't have an
> > example and desc DG didn't seem to help.
>
> Use the full atom name which is of the form:
>
> unit.res.atom name
>
> So for example for DG there is only one residue.
>
> Desc DG.1
>
> And in this the phosphorus atom is called P so you would use:
>
> set DG head DG.1.P
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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