Hello Amber users,
Am planning to do a matrix correlation analysis on some data. I know that an rms fit has to be done prior to this process using a reference structure.
I have some question:
1. Does it matter whether I place the reference file before I trajin my netcdf file or do I need to place it after I trajin my netcdf file? ( I plan to use the data in the netcdf file for the correlation analysis)
For example below is the input i plan to use for my analysis:
reference flp.inpcrd
trajin flp.netcdf 1 1000000000 1
rms TOFIRST :1&!.H= first out flp.agr mass
autoimage
center :1 origin mass
matrix correl name flp out Flp.dat .1 by atom
could it be:
trajin flp.netcdf 1 1000000000 1
reference flp.inpcrd
rms TOFIRST :1&!.H= first out flp.agr mass
autoimage
center :1 origin mass
matrix correl name flp out Flp.dat .1 byatom
2. Can i follow this with:
- analyze matrix
and
- analyze modes
to get the necessary data?
Thank you,
Silver
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Received on Thu Jan 01 2015 - 16:30:02 PST
