[gmx-users] question about minimisation

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,
I want to run a minimisation. But ONLY of the hydrogen atoms of my
protein. The rest of the structure shell be fix. This is very important
for the following analysis I want to do with it.

To make sure that the protein is fix I used the command:
genrestr

And choose the number 2 (Protein-H)  -> does this really mean that it
fixes the whole protein except of the hydrogen atoms?

The file looks like this:

; position restraints for Protein-H of GROtesk MACabre and Sinister

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
   5    1       1000       1000       1000
   6    1       1000       1000       1000
   7    1       1000       1000       1000
   8    1       1000       1000       1000
  11    1       1000       1000       1000


my PDB file of this part looks like this:

ATOM      1  CH3 ACE     5      25.060  31.190  21.020  1.00  0.00
ATOM      2 1HH3 ACE     5      24.950  30.330  20.510  1.00  0.00
ATOM      3 2HH3 ACE     5      24.680  31.950  20.490  1.00  0.00
ATOM      4 3HH3 ACE     5      26.040  31.350  21.180  1.00  0.00
ATOM      5  C   ACE     5      24.330  31.080  22.360  1.00  0.00
ATOM      6  O   ACE     5      24.350  32.030  23.140  1.00  0.00
ATOM      7  N   PRO     6      23.650  29.930  22.690  1.00  0.00
ATOM      8  CD  PRO     6      23.470  28.680  21.960  1.00  0.00
ATOM      9  HD1 PRO     6      24.330  28.170  21.960  1.00  0.00
ATOM     10  HD2 PRO     6      23.200  28.880  21.020  1.00  0.00
ATOM     11  CG  PRO     6      22.370  27.900  22.690  1.00  0.00


SO for me it looks like all the atoms except of the hydrogen atoms are fixed.


Additionally I have a membrane around my protein which also has to be
fixed. For this I use another restriction file containing only the lines:

[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000



But now my supervisor said that it seems like the whole protein is
minimised and not only the hydrogen atoms. How can that be? Or is it
possible that the whole protein is minimised although I have those
restriction files?
If I made an error in my minimisation please tell me!!

Thank you,
Eva