[AMBER] ptraj analysis problems - protein leaving the box

From: Daniel Scott <dscott5.nd.edu>
Date: Wed, 6 Jul 2011 12:14:43 -0400

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.

Dan Scott
Grad student, University of Notre Dame
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Received on Wed Jul 06 2011 - 09:30:05 PDT
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