Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS.
When I run pdb2gmx, using CHARMM27 FF, I had no error.
After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.itp
[
bondtypes ]
;
i j func b0 kb
SG
FE 1 0.232 209200.0
[
angletypes ]
;
i j k func th0 cth ub0 cub
CT2
SG FE 5 100.6 418.4 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
;
###
X
CS SS X 9 0.20 0.0 3
CA
CB SG FE 9 0.20 0.0 3
HB1
CB SG FE 9 0.20 0.0 3
HB1
CB SG FE 9 0.20 0.0 3
;
###
X
FE SS X 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
But after that, I had another type of error:
Fatal error:
Unknown bond_atomtype SG, I correct it by default.
after that in grompp step : I got error
ERROR 7 [file topol.top, line 41571]:
> No default Proper Dih. types
>
> Fatal error:
> There were 24 errors in input file(s).
what should I do?
>
Are the parameters taken from a CHARMM based force field?
It seems you have not included dihedral types for the modified parameters/atom names.
thanks Sayantan
I can correct them. I change atom type to Charmm forcefield. after this change, no error was seen.
thank you
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