On Thu, Aug 6, 2015 at 7:35 AM, Karolina Markowska <markowska.kar.gmail.com>
wrote:
> Dear Amber Users,
>
> I have a problem with cpptraj and it's autoimage command. My system
> consists of two chains and two Mn2+ ions. I usually use the script below,
> but when I use it on this system, something went wrong.
>
> reference protein_complex.inpcrd
> trajin emd2.traj.gz
> center :1-374 mass origin
> image origin center
>
These two commands are pointless here. Their effect is promptly
overwritten by the "autoimage" command.
> autoimage
> rms ToRef :1-374.CA,C,N= reference out rmsd_prod.arg mass
> atomicfluct out rmsf_prod.arg :1-374 byres
> trajout protein_complex_f.binpos binpos
> go
>
> I looks like only the first chain was centered. I've tried to change the
> autoimage command and put:
>
Yes, this is how "autoimage" works. In some cases it can result in a
waterbox that looks "shifted" compared to all of the chains, but I have
usually found that it suffices for my needs. If you really want all chains
to be centered in the box, then you should follow the "autoimage" command
with separate center and image commands (the ones I told you were pointless
above):
autoimage
center :1-374 mass origin
image origin center familiar
Note that the "familiar" here is because you are using a truncated
octahedron ("autoimage" takes care of that distinction by default, but with
the image command it's necessary). In this case, the "autoimage" command
will properly image the different chains with respect to each other, and
the following 'center' and 'image' commands will center all of the chains
in the unit cell and image the waters around that.
> autoimage anchor :1-374
>
If residues 1-374 are from a dimer (i.e., two distinct "molecules"), then
this is not a good thing to do. If they are imaged in separate boxes, then
this will prevent them from being imaged back into the same box.
> because I've read in the Amber Manual, that autoimage by default center
> only the first molecule, but after that the water box looked wierd.
>
You need to be more specific. There are a lot of ways that a water box can
look "weird". Here are some examples: http://www.shaman.ibpc.fr/heat.png,
http://ambermd.org/tutorials/basic/tutorial2/files/vmd_crdbox1.jpg (pretend
that applies to waters), ... and it's impossible to know what people
consider 'weird' and 'normal'.
One guess I have is that it looks like "chunks" are cut out of the corners
of the unit cell (like the first link I showed above), in which case that
problem arises because you did not use NpT to equilibrate the density,
leading to fictitiously low pressures and a simulation that is actually
*boiling* as a result. If I am mistaken, you would need to see an image so
we can see what you see.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 06 2015 - 06:30:02 PDT
