[gmx-users] protein-protein simulation

[Guido Leoni]

Dear List
I'm newbie to MD .
I'd like to simulate a protein protein binding dinamic between 2 proteins
of 500 aa each one. I have some very basic questions:
1) In order to setup my dinamic i'm following the basic tutorial on spider
toxin peptide (
http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems)
starting from a pdb with the 2 structures near each other and oriented
according to some docking calculations. Is this procedure a reasonable
starting point?

2)  I tryed to run the MD with the same  parameters of tutorial in my
md.mdp file (listed at the end of the mail). Should i set the contraints
parameter to "none"? In order to allow more flexibility of the side  chains?
Finally if the previous points are reasonable ...
3) In your opinion which could be a reasonable time to explore the
possibility that the 2 proteins bind each other? I'm  making some attempts
using 500 ps for now

Sorry for my silly questions and thank you very much for any kind of help
Best
Guido
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002 ; ps !
nsteps              =  50000 ; total 100.0 ps.
nstcomm             =  10
nstxout             =  500 ; collect data every 1.0 ps
nstxtcout           =  500
nstvout             =  5000
nstfout             =  0
nstlog              =  10
nstenergy           =  50
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype  =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.4
pme_order  =  4
ewald_rtol =  1e-5
optimize_fft =  yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl              =  v-rescale
tau_t               =  0.1 0.1
tc-grps  =  protein non-protein
ref_t               =  300 300
; Pressure coupling is off
Pcoupl              =  no
Pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5


-- 
Guido Leoni
National Research Institute on Food and Nutrition
(I.N.R.A.N.)
via Ardeatina 546
00178 Rome
Italy

tel     + 39 06 51 49 41 (operator)
        + 39 06 51 49 4498 (direct)
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