it sounds like you have 3 molecules, so you'd need a more complex script
than this. take a look through the archives for examples.
On Thu, Jun 28, 2012 at 3:52 PM, Wilson, Katie <ka.wilson.uleth.ca> wrote:
> My system is a DNA-protein complex which I have run 10 ns of production MD
> without restraints with constant pressure and temperature and with PBC. I
> am trying to calculate rmsd based on the protein's backbone and center it
> based on the protein resdides (resdiues 1-354).
>
> > you'll need to give more details, we don't know anything about your
> > system.
> >
> > On Thu, Jun 28, 2012 at 3:43 PM, Wilson, Katie <ka.wilson.uleth.ca>
> wrote:
> >
> >> I actually did used the image command before calcuating the rmsd and it
> >> didnt seem to make a difference. I used
> >>
> >> trajin md2.mdcrd 1 50000 10
> >> trajout strip.mdcrd
> >> center :1-354 mass origin
> >> image origin center
> >> rms first out rms.out .CA,C,N
> >>
> >> Katie
> >>
> >> > is it possible you're calculating the rmsd for a group that involves
> >> more
> >> > than 1 molecule? if yes, loko in the archives and the manual for the
> >> image
> >> > command.
> >> >
> >> > On Thu, Jun 28, 2012 at 3:22 PM, Wilson, Katie <ka.wilson.uleth.ca>
> >> wrote:
> >> >
> >> >> Hello,
> >> >> When I calculate the rmsd value with ptraj on AMBER 11 (rms first out
> >> >> rms
> >> >> .CA,C,N) the value jumps from 2 to 25 and then 25 to 500. What would
> >> >> cause
> >> >> these jumps to occur and how do I fix the rmsd calculation so these
> >> >> jumps
> >> >> do not occur?
> >> >> Thanks,
> >> >> Katie
> >> >>
> >> >>
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> >>
> >>
> >>
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Received on Thu Jun 28 2012 - 13:00:05 PDT
