RMS matrix with CARNAL

From: Margit Mollhoff <margit_at_telomere.lanl.gov>
Date: Fri 16 Nov 2001 13:09:22 -0600

Hi,

I've used CARNAL to produce a RMS matrix that compares each coordinate
set of my data stream (s1) to each coordinate set of my STATIC stream
(ref). I never could get a triangular matrix as you describe in your
AMBER 6 manual (Carnal module: RMS rmsid [FIT] groupid staticid [ATOM]
[RES]; page 303-304)
I get every time just a comparison to the first set within my STATIC
stream, or I can get a comparison to a single defined set (putting just
one file name in the definition for STATIC ref) but not a matrix as
wished and described.

The script I used is here:

FILES_IN
     PARM p1 prmtop;
     STREAM s1
      min10.xyz
      min20.xyz
      min30.xyz
      min40.xyz
      min50.xyz
      min60.xyz
      min70.xyz
      min80.xyz
      min90.xyz;
     STATIC ref
      min10.xyz
      min20.xyz
      min30.xyz
      min40.xyz
      min50.xyz
      min60.xyz
      min70.xyz
      min80.xyz
      min90.xyz;
FILES_OUT
     TABLE tbl test.rms;
DECLARE
     GROUP grp ( (ATOM NAME CA C N O)
                & (RES 1-235) );
     RMS fit FIT grp s1 ref;
OUTPUT
     TABLE tbl fit;
END


There is probably something wrong with the script! What ? I gave up
after a rather large number of unsuccessful tries to correct the script!

Please HELP !
Margit

(I wanted the RMS values for:
                      min10.xyz min20.xyz min30.xyz
min40.xyz min50.xyz ....
      min10.xyz 0
      min20.xyz something 0
      min30.xyz something ...
      min40.xyz ....
      min50.xyz
      min60.xyz
      min70.xyz
      min80.xyz
      min90.xyz)
Received on Fri Nov 16 2001 - 11:09:22 PST
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