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?

>

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