AMBER Archive (2003)

Subject: Re: Protein Reorientation (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Wed Mar 05 2003 - 12:05:11 CST

---------- Forwarded message ----------
Date: Wed, 05 Mar 2003 11:02:57 -0500
From: Michael Ford <mford_at_ccrc.uga.edu>
To: Carlos Simmerling <carlos.simmerling_at_stonybrook.edu>
Cc: Gemma Kinsella <maynooth_at_maths.tcd.ie>, amber_at_heimdal.compchem.ucsf.edu
Subject: Re: Protein Reorientation

Moil-view will not (in my experience) You need to use PyMol, including the
save_transformed script (which is on the net, or I can e-mail it).

Carlos Simmerling wrote:

> If you use my program MOIL-View, you can
> save the modified coordinates (including the
> rotation) to pdb format for use in leap.
> Keep in mind that Leap can also reorient
> the molecule (for example, using alignaxes).
> Carlos
>
> moil-view is on the AMBER distribution CD and
> also can be found at
> http://morita.chem.sunysb.edu/mlv.html
>
> ----- Original Message -----
> From: "Gemma Kinsella" <maynooth_at_maths.tcd.ie>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Cc: "Gemma Kinsella" <maynooth_at_maths.tcd.ie>
> Sent: Monday, March 03, 2003 8:54 AM
> Subject: Protein Reorientation
>
> > Hi all,
> >
> > I've come across what should be a trivial problem while trying to set up a
> > membranne protein simulation in a bilayer. I wish to reorientate the
> > position of my starting protein so it will lie straighter in the bilayer
> > during set-up. (i.e. loops at top and bottom)
> >
> > While I have no problem doing so visually, (weblab viewer, vmd, sybyl) I
> have
> > been unable to find a piece of software that will allow me to save the
> > proteins new coordinates to be introduced to leap and was hoping someone
> > could point me in the right direction.
> >
> > Many thanks,
> >
> > Gemma
> >
> >