Hi Dac,
Thank you for your help in this issue.
Silver
> On Dec 29, 2014, at 8:23 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>
>> On Mon, Dec 29, 2014, Sylvester Tumusiime wrote:
>>
>> I have a question regarding the use of rms fitting prior to performing
>> analyses like dihedral, atomicfluct and correlation.
>> I read in the amber tutorial 1:
>> /[1]http://ambermd.org/tutorials/analysis/tutorial1/
>> that "by default CPPTRAJ calculates the best-fit RMSD, which means each
>> structure is rotated and translated so as to minimize the RMSD to the
>> reference structure (in this case the first frame). As such, the 'rms'
>> command modifies coordinates for all subsequent commands unless 'nofit' is
>> specified"
>> therefore, if i am performing analysis using cpptraj, is it not necessary to
>> add the rms line. e.g.:
>> rms ToFirst :1-13&!.H= first out rmsd1.agr mass
>> prior to analysis since the co-ordinates will be modified again?
>
> I'm not sure what Dan (the tutorial author) meant by the term "by default"
> here: cpptraj only does an rms fit (and changes the coordinates) if you
> have an "rms line" in your script. So, yes, you (generally) need such
> a line for actions like atomicfluct and time correlation measurements.
>
> (Dihedrals don't change when the molecule is rotated or translated, so
> there it doesn't matter whether you have an rms command or not.)
>
> Thanks for asking the question: we'll update the tutorial to make this
> clearer.
>
> ....dac
>
>
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Received on Tue Dec 30 2014 - 13:00:02 PST
