VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sat Oct 29 2011 - 10:55:28 CDT

Look at:

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node20.html

You can use 'first ACE' 'last CT3'

You can align to principal axes using this script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

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
all]]]

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

[atomselect top all] move [trans x 45]

Also, these are usefull:

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node16.html

http://www.ks.uiuc.edu/Research/vmd/current/ug/node118.html

Good luck!

Gianluca

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 gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

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