AMBER Archive (2003)

Subject: AMBER: carnal

From: Frederico.Miranda_at_ibmb.uib.no
Date: Sun Oct 19 2003 - 14:48:06 CDT

Hye, I would like to mesure a distance between 2 atoms from a trajectory that
I got from a md simulation, but I can only mesure one distance, while I would
like to mesure the distance between the 2 atoms during the all trajectory.
Could someone help me please? Thank you.

PS: These are my input and output files for carnal:

INPUT:

FILES_IN
  PARM p1 pidimer.parm;
  STREAM s1 pidimer.mdcrd;
FILES_OUT
  TABLE tab1 pidimer.W120_W187_cALFA_dist.carnal;
DECLARE
  GROUP g1 (ATOM 1939);
  GROUP g2 (ATOM 5245);
  DIST dist1 g1 g2;
OUTPUT
  TABLE tab1 DIST;
END

OUTPUT:

                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin
> FILES_IN
> PARM p1 pidimer.parm;
Reading parm file (pidimer.parm)
parm: opening pidimer.parm
> STREAM s1 pidimer.mdcrd;
Using default parm (pidimer.parm) for STREAM s1
 (box will be read from stream)
stream: opening pidimer.mdcrd
> FILES_OUT
> TABLE tab1 pidimer.W120_W187_cALFA_dist.carnal;
> DECLARE
> GROUP g1 (ATOM 1939);
** Group g1: 1 atom
> GROUP g2 (ATOM 5245);
** Group g2: 1 atom
> DIST dist1 g1 g2;
> OUTPUT
> TABLE tab1 DIST;
> END
STREAM s1: no more files/crds (iteration 1)
SUMMARY
--Distance dist1: single 21.178

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