[AMBER] rms fit

From: Sylvester Tumusiime <stumusii.uno.edu>
Date: Mon, 29 Dec 2014 20:47:16 +0000

   Dear Amber users,
   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?
Thanks
Silver

References

   1. http://ambermd.org/tutorials/analysis/tutorial1/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 29 2014 - 13:00:05 PST
Custom Search