That makes sense--thanks!
Kristina
Quoting Petr Kulhanek <kulhanek.chemi.muni.cz>:
> Hello Kristina,
>
> >>>trajin test.crd 2 2
> >>>reference test.pdb.1
> >>>trajout pass.pdb pdb
> >>>image center familiar
> >>>rms first out rmsCheckPass :554
> >>>go
>
> >>>trajin test.crd 2 2
> >>>reference test.pdb.1
> >>>trajout fail.pdb pdb
> >>>rms first out rmsCheckFail :554
> >>>image center familiar
> >>>go
>
> rms fits selected residues by rotation of system. It means that also box
> is rotated. However image only works with original box orientation.
>
> So the corect order of actions is to perform image first and then rms.
> Therefore the second script is incorrect.
>
> If you use the second script then it can happen, in worst case, that
> solute will be overlaped with solvent. The introduced error only depends
> on how much the system is rotated by rms.
>
> Example script in amber manual is just example that works only and only
> if the system contains one solute molecule, water, and no counterions.
> Since the water is removed at the end, the error introduced by incorrect
> order of rms and image is eliminated.
>
> Best regards,
> Petr
>
> PS:
> if you want to use reference coordinates then you have to use
>
> rms reference out rmsCheckFail :554
>
>
>
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Received on Wed Jul 13 2005 - 20:53:00 PDT
