VMD-L Mailing List

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Wed Oct 30 2002 - 02:26:36 CST

Le Mardi 29 Octobre 2002 23:02, Marc Baaden a écrit :
> Thanks for your tip about ProFit. I already knew about the program and
> have used it. Actually I did not specify the actual purpose of my question.
> It is not my aim to reposition/change the coordinates of the system, I
> am merely doing snapshots within VMD, and want all of them to be centered
> on the protein in a certain view (the data is from MD simulations, so the
> protein moves around quite a bit ..).
>
> I could definitely do some fitting beforehand, but the easiest and nicest
> solution for me would be to do all in VMD without creating intermediate
> files.
>
> Thanks,
>
> Marc Baaden

If you are using an amber simulation, you can center your system on such an
alignment. So do the fit with carnal, and load it after in vmd.

I guess it is available in other modelling softwares.

Stef