[gmx-users] g-dist

[mohsen ramezanpour]

Dear All
I did the Enzyme/drug tutorial and generated complex.gro and complex.top
files as was said.
Now I want to measure the distance between center of mass of protein and
drug
I used g_dist but I could not.
I entered these commands(of course I made an index.ndx and g-dist.tpr):

I used from an typical .mdp file to generate .tpr file by below command:

grompp  -c complex.gro     -p   complex.top   -o  g-dist.tpr          -f
g-dist.mdp    -maxwarn 3
then,
g_dist     -f    complex.gro    -s   g-dist.tpr    -o  g-dist.xvg

but the result was an empty g-dist.xvg and:

Fatal error:
Unexpected end of file in file   631LIG  C12     45  -0.475  -0.514  -0.434
at line 2
(Source file ../../../../src/gmxlib/confio.
c, line 725)

besides,I want to measure this distance befor erunning and as a vector.
below is a part of my complex.gro:
  631LIG  F1      42  -0.701  -0.571  -0.151
  631LIG  C16     43  -0.534  -0.501  -0.306
  631LIG  H16     44  -0.491  -0.434  -0.232
  631LIG  C12     45  -0.475  -0.514  -0.434
  631LIG  H12     46  -0.394  -0.446  -0.459


thanks in advances
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