[gmx-users] Insertion of protein in lipid bilayer

[naga raju]

Dear gmx-users,
               I downloaded DPPC lipid bilayer from
http://www.lce.hut.fi/research/polymer/downloads.shtml
and dppc.itp,lipid.itp files from 
http://moose.bio.ucalgary.ca/index.php?page=Downloads.
To make hole I used the following steps:

1) perl make_hole.pl -f dppc.pdb -o outbilayer.pdb -r
1.4 -lipat P8 -lipid DPPC -cx 3.2 -cy 3.2 

2)prepared .trp file using the following parameters:
Here i took (dppc.pdb) the initial structure.
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000	; total 10 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  DPP	SOL
tau_t               =  0.1	0.1
ref_t               =  300	300
; Energy monitoring
energygrps          =  DPP  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

3) next i run the mdrun command.

 mdrun -v -hole -holep hp.mdp -s ***.tpr 

Here is my hp.mdp file

holetype                 = Cyl
hfm                      = 50
supf                     = 20
hr			 = 4.0 
hx			 = 3.2
hy			 = 3.2
hz			 = 3.4
hp1 			 = 1
hp2 			 = 6400
s1 			 = 6401
s2			 = 17365
hz1 			 = 3.0
hz2 			 = 6.3
sfm 			 = 10.0 
sofs			 = 0.15 
molsurf_file             = 
debugsurf 		 = no
resforces  		 = yes

Here are my doubts:

1) To genarate *.tpr file which pdb file to be taken,
initial structure or generated by make_hole.pl
program.
 
2)After doing above process, i couldn't see the hole
in the molecule. Could you tell me the correct
procedure.

    
     
 Thank you for spending your valuable time to read
this mail.


                 bye
                            nagaraju


		
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