From: Gianluca Interlandi (
Date: Sat Oct 29 2011 - 10:55:28 CDT

Look at:

You can use 'first ACE' 'last CT3'

You can align to principal axes using this script:

You can also move it and rotate it yourself using the 'moveby' and 'move'
commands, e.g.,

This will center the system (e.g., protein + X-ray water) Note that the
line might be wrapped and you have to enter it in one line:

[atomselect top all] moveby [vecscale -1 [measure center [atomselect top

This will rotate around the x axis for a given angle (45 dgrees in this

[atomselect top all] move [trans x 45]

Also, these are usefull:

Good luck!


On Sat, 29 Oct 2011, James Starlight wrote:

> Dear VMD users!
> I have some question about processing of my starting structure for further MD simulation.
> I'd like to prepare my initial structure in VMD but run si,ulation via other package.
> I wounder to know
> 1)is it possible to add CAP groups like ACE or NH2 on the C and N- term ressidues?
> 2) to orient ( align) my protein along chozen axis.?
> Thank you for your help
> James

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.