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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