AMBER Archive (2004)

Subject: AMBER: center of mass in CARNAL

From: Herbert Georg (
Date: Thu Feb 12 2004 - 10:15:17 CST

I have noticed that when I declare a GROUP in the DECLARE section and
then I try to print in a TABLE the group's geometric center and the
center of mass, it seems that Carnal is printing the geometric center
twice simply. Also, probably important to say, my table.c was replaced
by a new one produced by Bill Ross to fix a problem with the TABLE
command. My is the following:

# Calcula vetores normais aos planos definidos pelos pontos O14 O34 O54
e O24 O44 O64.
  PARM p1;
  STREAM s1 md.crd.gz;

  TABLE tab1;
  TABLE tab2;

  GROUP g1 ((RES 1) & (ATOM NAME O14 O24 O34 O44 O54 O64));
  PLANE n1 O14 1 g1 O24 1;
  PLANE n2 O14 1 g1 O34 1;
  PLANE n3 O54 1 g1 O14 1;
  PLANE n4 O64 1 g1 O14 1;
  PLANE n5 O24 1 g1 O34 1;
  PLANE n6 O24 1 g1 O44 1;
  PLANE n7 O64 1 g1 O24 1;
  PLANE n8 O34 1 g1 O44 1;
  PLANE n9 O34 1 g1 O54 1;
  PLANE n10 O44 1 g1 O54 1;
  PLANE n11 O44 1 g1 O64 1;

# TABLE tab1 n1 n2 n3 n4 n5 n6 n7 n8 n9 n10 n11 g1%center g1%cmass;
  TABLE tab2 g1%center g1%cmass;


And a sample of the file

L0 8.316667e-02 -3.883333e-02 -2.816667e-01 8.316667e-02 -3.883333e-02
L0 3.800000e-02 -3.000000e-02 -3.418333e-01 3.800000e-02 -3.000000e-02
L0 9.900000e-02 -2.766667e-02 -2.888333e-01 9.900000e-02 -2.766667e-02
L0 4.783333e-02 -4.150000e-02 -4.075000e-01 4.783333e-02 -4.150000e-02
L0 7.283333e-02 -8.883333e-02 -4.055000e-01 7.283333e-02 -8.883333e-02
L0 7.616667e-02 -5.483333e-02 -3.205000e-01 7.616667e-02 -5.483333e-02

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