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
