[gmx-users] HEME-cysteine gromacs simulation

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Aug 26 05:10:17 CEST 2009

You always need a correct topology. The main issue here is that you  
need to have correct parameters. Where did you get your heme and Fe  
parameters? Were you careful about the Fe state oxidation state? I  
suspect that most people use Amber because of their antechamber  
program, which seems like a brilliant idea even if it may overstretch  
it's own parameterization without letting you know. I have no specific  
advice for you here beyond saying that it is worth spending a month  
figuring out what parameters you should really be using (hint: why  
would you be using ffG43a1 if most others use Amber here? do you know  
something that they don't?). This will end up saving you time in the  
long run.

Note that ffG43a1 is the GROMOS forcefield, not the  GROMACS  
forcefield. It is unfortunate that many programs (Amber, Charmm,  
gromacs) have their own similarly named forcefield, but that does not  
mean that the forcefield must be used with the associated program.  
There are forcefields that are not associated with a program (OPLS)  
and programs that never developed their own force field (NAMD,  
Desmond, Tinker, LAMMPS), so it is perfectly ok for you to use the  
amber forcefield with the gromacs program.

Bottom line: read, read, read.


-- original message --

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  

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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