VMD-L Mailing List

From: Gemma Kinsella (maynooth_at_maths.tcd.ie)
Date: Mon Mar 03 2003 - 08:39:51 CST

Hi all,

I wish to reorientate the position of my starting membrane protein so it will
lie straighter in a bilayer for a molecular dynamics simulation. (i.e. loops
at top and bottom)

While I have no problem doing so visually, (vmd, sybyl) I have been unable to
find a piece of software that will allow me to save the proteins new
coordinates. I've been advised this can be achieved through calculating
the transformation matrix used to reorient the protein with vmd. This same
transformation matrix can then be applied to the original orientation within
Amber. Does anyone have any insights as to how to go about this??? I am a
little confused with the trans options and implimentations.

Many thanks,
Gemma