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
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