[gmx-users] How to make a TM protein - Help
Marcos Villarreal
arloa at dqb.fcq.unc.edu.ar
Mon Jul 22 19:27:51 CEST 2002
Dear John,
Here is a simple protocol to make a hole in a membrane.
1) take an equilibrated membrane and remove the water and some lipids in the
center. If your helix has an cross molecular area of about 1.5 nm^2 you
should remove 2 dppc per monolayer (area 0.64 nm^2)
2) manually insert in the pdb a "string" of atoms called XXX (fig 1)
3) link the XXX atoms by bonds and define a repulsive interaction with the
rest of the atoms in your system.(xxx.itp)
4) minimize and perform a series of MD with position restrains in the XXX
atoms and gradually increasing the repulsive force .
Some tricks:
-You should probably have to move some torsion angles in some lipids chains
before you can get a "clear path" where to put the XXX atoms. This can be
done with rasmol (settings-> pick bond; settings ->rotate bond)
-In the first MD you should probably have to use a short timestep (0.5 fs)
and low temperature (100K).
-Use PBC, NVT and don't go beyond about 200 ps in total (in step 4) because
the rest of the membrane could be deformed.
-Once you get a fine hole, put back the water molecules. Equilibrate them an
perform some annealing in the lipid chains. ie put the lipids at 450K while
the water stay at 330K or something like this. Then cool down the lipids
gradually. This step is important to remove some possible bad lipid chains
conformation.
-you are ready to insert you peptide in the system.
I hope this can help you.
Saludos,
--
Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.
-------------------------------------------------------
--
Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.
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[ atomtypes ]
;name mass charge ptype c6 c12
;
XXX 2000.00 0.000 A 0.00000e+00 1.00000e-07 carbonyl O, OPLS
[ nonbond_params ]
; i j func c6 c12
LO XXX 1 0.00000e+00 1.00000e-07
LOM XXX 1 0.00000e+00 1.00000e-07
LNL XXX 1 0.00000e+00 1.00000e-07
XXX OW 1 0.00000e+00 1.00000e-07
XXX LC 1 0.00000e+00 1.00000e-07
XXX LH1 1 0.00000e+00 1.00000e-07
XXX LH2 1 0.00000e+00 1.00000e-07
XXX LP 1 0.00000e+00 1.00000e-07
XXX LOS 1 0.00000e+00 1.00000e-07
XXX LP2 1 0.00000e+00 1.00000e-07
XXX LP3 1 0.00000e+00 1.00000e-07
XXX LC3 1 0.00000e+00 1.00000e-07
XXX LC2 1 0.00000e+00 1.00000e-07
XXX HW 1 0.00000e+00 1.00000e-07
[ moleculetype ]
; Name nrexcl
XXX 10
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 XXX 1 XXX XXX 1 0 20000.000
2 XXX 2 XXX XXX 1 0 20000.000
3 XXX 3 XXX XXX 1 0 20000.000
4 XXX 4 XXX XXX 1 0 20000.000
5 XXX 5 XXX XXX 1 0 20000.000
6 XXX 6 XXX XXX 1 0 20000.000
7 XXX 7 XXX XXX 1 0 20000.000
8 XXX 8 XXX XXX 1 0 20000.000
9 XXX 9 XXX XXX 1 0 20000.000
10 XXX 10 XXX XXX 1 0 20000.000
11 XXX 11 XXX XXX 1 0 20000.000
12 XXX 12 XXX XXX 1 0 20000.000
13 XXX 13 XXX XXX 1 0 20000.000
14 XXX 14 XXX XXX 1 0 20000.000
15 XXX 15 XXX XXX 1 0 20000.000
16 XXX 16 XXX XXX 1 0 20000.000
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.4 500000
2 3 1 0.4 500000
3 4 1 0.4 500000
4 5 1 0.4 500000
5 6 1 0.4 500000
6 7 1 0.4 500000
7 8 1 0.4 500000
8 9 1 0.4 500000
9 10 1 0.4 500000
10 11 1 0.4 500000
11 12 1 0.4 500000
12 13 1 0.4 500000
13 14 1 0.4 500000
14 15 1 0.4 500000
15 16 1 0.4 500000
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
2 1 100000 100000 100000
3 1 100000 100000 100000
4 1 100000 100000 100000
5 1 100000 100000 100000
6 1 100000 100000 100000
7 1 100000 100000 100000
8 1 100000 100000 100000
9 1 100000 100000 100000
10 1 100000 100000 100000
11 1 100000 100000 100000
12 1 100000 100000 100000
13 1 100000 100000 100000
14 1 100000 100000 100000
15 1 100000 100000 100000
16 1 100000 100000 100000
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