Thank you very much for your answer.
Switching the autoimage command above the center and image command worked
for me.
>autoimage
>center :1-374 mass origin
>image origin center familiar
My 'weird' water isn't shown at any of your examples. It comes out, that my
'weird' water was the 'triclinic' water. If I may ask, what's the utility
of that kind of water representation?
Thank you once again for your help.
Best regards,
KM
2015-08-06 15:19 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> 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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> AMBER.ambermd.org
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>
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Received on Fri Aug 07 2015 - 03:00:03 PDT
