?????? 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.
Mark
[ 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
.........
??????????????????????,www.yeah.net
??????????????????????,www.yeah.net
------------------------------------------------------------------------
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