AMBER Archive (2008)

Subject: Re: AMBER: imaging problem

From: David Smith (David.Smith_at_irb.hr)
Date: Tue Apr 15 2008 - 08:30:48 CDT

Marcin,

I had a similar problem once.

Make sure your stripped topology contains a box as well. It seems that
this sets some flag in ptraj without which the imaging doesn't work
properly.

I can't remember anymore whether I used modifyBoxInfo in rdparm or
manually added the box in leap. Both should do the trick.

Good luck.

David.

On Tue, 2008-04-15 at 14:16 +0100, Marcin Krol wrote:
> 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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-- 
Dr. David Smith 
Division of Organic Chemistry and Biochemistry 
Rudjer Boskovic Institute 
Bijenicka 54 
10002 Zagreb, Croatia 
Tel:  +385 1 456 1182 
Fax1: +385 1 456 1182 
Fax2: +385 1 456 1118

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