> I want to align several trajectories to a reference frame as follows:
>
> trajin prod.10ps_steps.mdcrd 1 1000 1
> reference ref.pdb
> rms reference .CA,C,N
> trajout prod.10ps_steps.aligned.mdcrd
>
> Unfortunately, this works for some, but not all of my trajectories (as
> can be seen in the attached file). Of course, I'm surely using the same
> reference frame for all alignments.
It is not clear what you think the problem is; all of those structures
look fairly well aligned; moreover, during the MD the structures will
move so the alignment will not be perfect...
Perhaps what you are stating with the attached figure is that the
structures on the lower right should overlap with those on the upper left?
If this is the case, do make sure the same ref.pdb is used each time and
was not overwritten by one of the scripts. Also make sure that ptraj did
not complain about loading the reference structure in. The only possible
other explanation I can think of is that the tube molecule has C,CA,N
atoms and there was an imaging issue...
Note that you can do the fitting all in one ptraj run...
trajin prod.10ps_steps.mdcrd 1 1000 1
trajin prod.10ps_steps.mdcrd.1 1 1000 1
trajin prod.10ps_steps.mdcrd.2 1 1000 1
reference ref.pdb
rms reference .CA,C,N
trajout prod.10ps_steps.aligned.mdcrd
--tec3
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Received on Thu Feb 25 2010 - 13:00:03 PST
