AMBER Archive (2008)

Subject: Re: AMBER: imaging problem

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Tue Apr 15 2008 - 08:16:01 CDT

Thanks
It works beautifully on original trajectories (protein+water+ions,
trajectory file with PBC info). However, it doesn't work on trajectories
with removed water and ions but _with_ PBC info present (I generated no
water trajectories without nobox keyword). Don't know why, but at least
it works for the original ones
Many thanks
Marcin
> each time you center, try keeping everything already centered in the mask.
> for example, do 1:326, then 1:652, etc.
>
> On Tue, Apr 15, 2008 at 7:54 AM, Marcin Krol <krol01_at_cancer.org.uk
> <mailto:krol01_at_cancer.org.uk>> wrote:
>
> Dear All,
>
> I've run a 10ns MD simulation of a tetrameric protein in explicit
> solvent (PBC). I used iwrap=1. Still different monomers jump away
> from the others, then go back - I assume they jump to other
> periodic cells. I tried to put all monomers back to the primary
> unit cell. I used a modified ptraj script suggested some time ago
> by Prof. Cheatham (bring first molecule to the origin, image, then
> center the whole solute and image again, script given below).
> Since I have four monomers, I centred and imaged each monomer
> separately and then the whole molecule. But it doesn't put the
> monomers back to the primary cell. It shifts the whole system
> (probably because of the multiple center keywords), but the
> tetramer is still disrupted (3rd monomer 653-978 in another
> periodic cell). I tried different commands (imgining by mask, with
> origin center, without origin, etc) but never managed to get the
> whole tetramer back together.
> Can someone tell me what is going wrong? Any help will be great!
>

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