Egidijus Kuprusevicius wrote:
Hello, could anyone help me and check if the topology of the HEO compound was
done properly for G96 ff? Thanks in advance. I couldn't find it in the
database, so I decided to try to make it manualy. Any comments would be
appreciated. Or maybe does exists any programs who does the work?
It would help to know what "HEO" is, and which version of Gromos96 you are
attempting to use. If this is some sort of HEME derivative, as it appears, you
can probably verify much of the topology, since HEME exists in the .rtp file for
all the Gromos96 variants.
It is not possible to simply look at a topology and verify if it is correct.
Parameterization requires you to verify some sort of experimental observable to
justify the parameters you have assigned.
-Justin
[ HEO ]
[ atoms ]
FEFE 0.4 0
NANR-0.1 0
NBNR-0.1 0
NCNR-0.1 0
NDNR-0.1 0
CHA CH1 0.0 1
C1A C 0.0 2
C2A C 0.0 2
C3A C 0.0 2
C4A C 0.0 2
CMA CH3 0.0 3
CAA CH2 0.0 4
CBA CH2 0.0 4
CGA C 0.27000 5
O1AOM-0.63500 5
O2AOM-0.63500 5
CHB CH1 0.0 6
C1B C 0.0 7
C2B C 0.0 7
C3B C 0.0 7
C4B C 0.0 7
CMB CH3 0.0 8
C11 C 0.38000 9
O11 O-0.38000 9
CHC CH1 0.010
C1C C 0.011
C2C C 0.011
C3C C 0.011
C4C C 0.011
CMC CH3 0.012
CAC CR1 0.013
CBC CH2 0.013
CHD CH1 0.014
C1D C 0.015
C2D C 0.015
C3D C 0.015
C4D C 0.015
CMD CH3 0.016
CAD CH2 0.017
CBD CH2 0.017
CGD C 0.2700018
O1DOM-0.6350018
O2DOM-0.6350018
C12 CH2 0.019
C13 CH2 0.019
C14 CH2 0.020
C15 CH1 0.020
C16 CH3 0.020
C17 CH2 0.020
C18 CH2 0.021
C19 CH2 0.022
C20 CH1 0.022
C21 CH3 0.022
C22 CH2 0.022
C23 CH2 0.023
C24 CH2 0.024
C25 CH1 0.024
C26 CH3 0.024
C27 CH3 0.024
[ bonds ]
FENAgb_34
FENBgb_34
FENCgb_34
FENDgb_34
NA C1Agb_13
NA C4Agb_13
NB C1Bgb_13
NB C4Bgb_13
NC C1Cgb_13
NC C4Cgb_13
ND C1Dgb_13
ND C4Dgb_13
CHA C1Agb_16
CHA C4Dgb_16
C1A C2Agb_16
C2A C3Agb_16
C2A CAAgb_26
C3A C4Agb_16
C3A CMAgb_26
C4A CHBgb_16
CAA CBAgb_26
CBA CGAgb_26
CGA O1Agb_5
CGA O2Agb_5
CHB C1Bgb_16
C1B C2Bgb_16
C2B C3Bgb_16
C2B CMBgb_26
C3B C4Bgb_16
C4B CHCgb_16
CHC C1Cgb_16
C1C C2Cgb_16
C2C C3Cgb_16
C2C CMCgb_26
C3C C4Cgb_16
C3C CACgb_26
C4C CHDgb_16
CAC CBCgb_11
CHD C1Dgb_16
C1D C2Dgb_16
C2D C3Dgb_16
C2D CMDgb_26
C3D C4Dgb_16
C3D CADgb_26
CAD CBDgb_26
CBD CGDgb_26
CGD O1Dgb_5
CGD O2Dgb_5
C3B C11gb_26
C11 O11gb_4
C11 C12gb_26 ; C, CHn - C, CHn800
C12 C13gb_26 ; C, CHn - C, CHn800
C13 C14gb_26 ; C, CHn - C, CHn800
C14 C15gb_26 ; C, CHn - C, CHn800
C15 C16gb_26 ; C, CHn - C, CHn800
C15 C17gb_26 ; C, CHn - C, CHn800
C17 C18gb_26 ; C, CHn - C, CHn800
C18 C19gb_26 ; C, CHn - C, CHn800
C19 C20gb_26 ; C, CHn - C, CHn800
C20 C21gb_26 ; C, CHn - C, CHn800
C20 C22gb_26 ; C, CHn - C, CHn800
C22 C23gb_26 ; C, CHn - C, CHn800
C23 C24gb_26 ; C, CHn - C, CHn800
C24 C25gb_26 ; C, CHn - C, CHn800
C25 C26gb_26 ; C, CHn - C, CHn800
C25 C27gb_26 ; C, CHn - C, CHn800
[ exclusions ]
; aiaj
FE CHA
FE C2A
FE C3A
FE CHB
FE C2B
FE C3B
FE CHC
FE C2C
FE C3C
FE CHD
FE C2D
FE C3D
NA CMA
NA CAA
NA C1B
NA C4B
NA C1C
NA C4C
NA C1D
NA C4D
NB C1A
NB C4A
NB CMB
NB C11
NB C1C
NB C4C
NB C1D
NB C4D
NC C1A
NC
