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.
Chris.
-- 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
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
.........
ûÓйã¸æµÄÖÕÉíÃâ·ÑÓÊÏä,www.yeah.net
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