[gmx-users] HEME-cysteine gromacs simulation

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 26 04:46:24 CEST 2009

¹ù½¨Â· wrote:
> 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.

Visualization programs have to use heuristics to guess where bonds are 
and what names occur for which atoms (HG1 might be mercury or the first 
hydrogen on a gamma carbon, NE might be neon or an epsilon nitrogen, 
etc.). Only if you are able to read in a .tpr (such as with ngmx 
distributed inside GROMACS) can you get any visual confirmation of what 
GROMACS thinks you have described in your topology. There is no 
standardized widely-used mechanism for including such information in a 
PDB file, and so such usage of a file is unreliable.

> 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¡£

Read the .log files as well. GROMACS almost never segfaults (except when 
subjected to buggy MPI libraries), and when it does it will normally 
write some diagnostic information to stdout or the .log file.

> 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?

Sorry, I can't help there.

> 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?)

Look at the results in ngmx to get started. Try generating a structure 
for some minimalist version of the heme group and get EM and MD to work 
on that first. If you reduce the complexity, you can eliminate potential 
sources of problems until you find the source.


> [ 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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