AMBER Archive (2008)

Subject: Re: AMBER: imaging problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Apr 15 2008 - 07:22:18 CDT

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> 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!
>
> Many thanks
> Marcin
>
> My script is given below:
>
> trajin N-md100.nowat.crd 1 1000 50
> trajout N_md100.repacked.crd trajectory
>
> center :1-326 mass origin
> image origin center
>
> center :327-652 mass origin
> image origin center
>
> center :653-978 mass origin
> image origin center
>
> center :979-1304 mass origin
> image origin center
>
> center :1-1304 mass origin
> image origin center
>
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