[gmx-users] HEME-cysteine gromacs simulation

[郭建路]

HI all:

I want to run a simulation with  heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Befor runing the gromacs molecular simulation,i define the heme group as a new residue in the .rtp files,following the required formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new FE-S bong.

i run the simulation like this:

pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce       
editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9                                       
genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top                              
grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr                                      
genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr 
grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr                                      
mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr                               
grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr                                      
mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log     

 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the bonds between FE-S &FE-N,i add or delete a blank space befor or after the FE in the pdb file,it was read as iron(FE) again but still missing;when checking the .top file,there was a FE (both atom name and type)and formed the FE-S & FE-N bonds.

if i ignore the above things,go on the command ,when runing the em.mdp there is a tip that Steepest Descents failed converged to Fmax < 1000 in 5001 steps.when run the pr.tpr,a error emerged as segment fatal error。

2 someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Does anyone known a paper with a gromacs force field for HEME group?

please help me how handle those problems,how can i go on the simulation?

the HEME-cysteine parameter in the rtp files,define themas a new residue.(is there any problems?)

[ HEME ]                             
 [ atoms ]                           
    N     N    -0.28000     0        
    H     H     0.28000     0        
   CA   CH1     0.00000     1        
   CB   CH2    -0.10000     2        
   SG     S    -0.40000     2        
    C     C     0.38000     3        
    O     O    -0.38000     3        
   FE    FE     0.84700     4        
   NA    NR    -0.37000     4        
   NB    NR    -0.42300     4        
   NC    NR    -0.50400     4        
........
 [ bonds ]                           
    N     H    gb_2                  
    N    CA    gb_20                 
   CA     C    gb_26                 
    C     O    gb_4                  
    C    +N    gb_9                  
   CA    CB    gb_26                 
   CB    SG    gb_30                 
   SG    FE    gb_48                 
   FE    NA    gb_34                 
   FE    NB    gb_34                 
   FE    NC    gb_34                 
   FE    ND    gb_34   

.........              
 [ angles ]                          
;  ai    aj    ak   gromos type      
   -C     N     H     ga_31          
    H     N    CA     ga_17          
   -C     N    CA     ga_30          
    N    CA     C     ga_12          
   CA     C    +N     ga_18          
   CA     C     O     ga_29                  
 .......           
 [ impropers ]                       
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1     
    C    CA    +N     O     gi_1     
   CA     N     C    CB     gi_2     
   FE    SG    NA    ND     gi_3     
   FE    SG    NA    NB     gi_3     
   FE    SG    NB    NC     gi_3     
   FE    SG    NC    ND     gi_3     
  .........     
 [ dihedrals ]                       
;  ai    aj    ak    al   gromos type
  .........


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