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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Received on Sun Oct 19 2003 - 20:53:01 PDT
