Re: [AMBER] ptraj analysis problems - protein leaving the box

From: Daniel Roe <>
Date: Wed, 6 Jul 2011 13:06:18 -0400


When dealing with molecules that have separated during the course of a
simulation due to wrapping (such as when 2 strands of DNA separate), I
often find I have to do more than 1 set of center/image commands to
get things back together - it makes sense if you think about it for a
bit, but I know that I personally find it hard to wrap my mind around
the idea of imaging sometimes (no pun intended I swear).

I'm assuming that 1-368 includes both monomers, so that 1-184 is
monomer 1 and 185-368 is monomer 2. I'm also assuming you have a
truncated octahedral box (hence use of the 'familiar' keyword). Try
center :1-184 origin mass
image center origin familiar
center :1-368 origin mass
image center origin familiar

I would run a short (i.e. trajin B7noWATnoNa200nsvsbound.mdcrd.gz 1 1)
test run with these commands (along with a trajout) to see if the
imaging was performed correctly before you run the larger calculation.
Let me know if you have any more problems. Good luck!


On Wed, Jul 6, 2011 at 12:14 PM, Daniel Scott <> wrote:
> Hi all,
> I spotted problems while analyzing an MD simulation of a heterodimeric
> protein, where the rmsd distance versus a reference structure had
> intermittent spikes.  At one of those time frames, I took a snapshot
> pdb which confirmed that the molecule was drifting outside the box.  As one
> monomer was more outside the primary box than the other, this monomer was
> moved to the other side of the primary box, separating it from the other
> monomer.  This explains the rmsd spikes, yet i am using the "center" and
> "image" commands that I thought would prevent this problem from happening in
> the first place.  The reference I am fitting to ("B7complextleap.pdb") is
> also centered in the box, so this adds to my confusion!  Specifically, my
> job script was:
> ------------------------------------------------------------------------------------------------------------
> trajin B7noWATnoNa200nsvsbound.mdcrd.gz
> center :1-368 mass
> image center :1-368 bymask familiar
> reference B7complextleap.pdb
> rms reference out B7vsbound200ns.rms :1-368.CA,C,N
> atomicfluct out B7bfactorN200ns.apf .N byatom bfactor
> atomicfluct out B7bfactorCA200ns.apf .CA byatom bfactor
> atomicfluct out B7bfactorC200ns.apf .C byatom bfactor
> atomicfluct out B7bfactorO200ns.apf .O byatom bfactor
> trajout B7noWATnoNa200nsvsboundnoorigin.mdcrd nobox
> ------------------------------------------------------------------------------------------------------------
> Please give any advice on how to eliminate this box-shifting problem.
> Thanks,
> Dan Scott
> Grad student, University of Notre Dame
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Received on Wed Jul 06 2011 - 10:30:03 PDT
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