[gmx-users] itp or top parameters for HEM?
Florent Hédin
work at fhedin.com
Tue Jun 7 21:31:37 CEST 2016
Hi,
I have added the following parameters from CHARMM 36 forcefield, may be
you can at least use them
as source of inspiration
[merged.hdb file]
...
HEME 16
2 6 HAA CAA CBA C2A
2 6 HAD CAD CBD C3D
2 6 HBA CBA CGA CAA
2 6 HBD CBD CGD CAD
2 3 HBB CBB CAB C3B
2 3 HBC CBC CAC C3C
3 4 HMA CMA C3A C4A
3 4 HMB CMB C2B C3B
3 4 HMC CMC C2C C3C
3 4 HMD CMD C2D C1D
1 1 HA CHA C1A C4D
1 1 HB CHB C1B C4A
1 1 HC CHC C1C C4B
1 1 HD CHD C1D C4C
1 2 HAB CAB C3B C2B
1 2 HAC CAC C3C C2C
...
[merged.rtp file]
...
[ HEME ]
[ atoms ]
FE FE 0.240 0
NA NPH -0.180 1
NB NPH -0.180 2
NC NPH -0.180 3
ND NPH -0.180 4
C1A CPA 0.120 5
C2A CPB -0.060 6
C3A CPB -0.060 7
C4A CPA 0.120 8
C1B CPA 0.120 9
C2B CPB -0.060 10
C3B CPB -0.060 11
C4B CPA 0.120 12
C1C CPA 0.120 13
C2C CPB -0.060 14
C3C CPB -0.060 15
C4C CPA 0.120 16
C1D CPA 0.120 17
C2D CPB -0.060 18
C3D CPB -0.060 19
C4D CPA 0.120 20
CHA CPM -0.100 21
HA HA 0.100 22
CHB CPM -0.100 23
HB HA 0.100 24
CHC CPM -0.100 25
HC HA 0.100 26
CHD CPM -0.100 27
HD HA 0.100 28
CMA CT3 -0.270 29
HMA1 HA3 0.090 30
HMA2 HA3 0.090 31
HMA3 HA3 0.090 32
CAA CT2 -0.180 33
HAA1 HA2 0.090 34
HAA2 HA2 0.090 35
CBA CT2 -0.280 36
HBA1 HA2 0.090 37
HBA2 HA2 0.090 38
CGA CC 0.620 39
O1A OC -0.760 40
O2A OC -0.760 41
CMB CT3 -0.270 42
HMB1 HA3 0.090 43
HMB2 HA3 0.090 44
HMB3 HA3 0.090 45
CAB CE1 -0.150 46
HAB HE1 0.150 47
CBB CE2 -0.420 48
HBB1 HE2 0.210 49
HBB2 HE2 0.210 50
CMC CT3 -0.270 51
HMC1 HA3 0.090 52
HMC2 HA3 0.090 53
HMC3 HA3 0.090 54
CAC CE1 -0.150 55
HAC HE1 0.150 56
CBC CE2 -0.420 57
HBC1 HE2 0.210 58
HBC2 HE2 0.210 59
CMD CT3 -0.270 60
HMD1 HA3 0.090 61
HMD2 HA3 0.090 62
HMD3 HA3 0.090 63
CAD CT2 -0.180 64
HAD1 HA2 0.090 65
HAD2 HA2 0.090 66
CBD CT2 -0.280 67
HBD1 HA2 0.090 68
HBD2 HA2 0.090 69
CGD CC 0.620 70
O1D OC -0.760 71
O2D OC -0.760 72
[ bonds ]
FE NA
FE NB
FE NC
FE ND
NA C1A
C1A C2A
C2A C3A
C3A C4A
NA C4A
C2A CAA
CAA CBA
CBA CGA
CGA O1A
CGA O2A
C3A CMA
CHB C4A
CHB C1B
NB C1B
C1B C2B
C2B C3B
C3B C4B
NB C4B
C2B CMB
C3B CAB
CAB CBB
CHC C4B
CHC C1C
NC C1C
C1C C2C
C2C C3C
C3C C4C
NC C4C
C2C CMC
C3C CAC
CAC CBC
CHD C4C
CHD C1D
ND C1D
C1D C2D
C2D C3D
C3D C4D
ND C4D
C2D CMD
C3D CAD
CAD CBD
CBD CGD
CGD O1D
CGD O2D
CHA C4D
CHA C1A
CHA HA
CHB HB
CHC HC
CHD HD
CAA HAA1
CAA HAA2
CBA HBA1
CBA HBA2
CMA HMA1
CMA HMA2
CMA HMA3
CMB HMB1
CMB HMB2
CMB HMB3
CAB HAB
CBB HBB1
CBB HBB2
CMC HMC1
CMC HMC2
CMC HMC3
CAC HAC
CBC HBC1
CBC HBC2
CMD HMD1
CMD HMD2
CMD HMD3
CAD HAD1
CAD HAD2
CBD HBD1
CBD HBD2
[ impropers ]
C2A C1A C3A CAA
C3A C2A C4A CMA
C2B C1B C3B CMB
C3B C2B C4B CAB
C2C C1C C3C CMC
C3C C2C C4C CAC
C2D C1D C3D CMD
C3D C2D C4D CAD
CGA CBA O2A O1A
CGD CBD O2D O1D
C4A NA C1A C2A
C1A NA C4A C3A
C4B NB C1B C2B
C1B NB C4B C3B
C4C NC C1C C2C
C1C NC C4C C3C
C4D ND C1D C2D
C1D ND C4D C3D
NA C1A C2A C3A
NA C4A C3A C2A
NB C1B C2B C3B
NB C4B C3B C2B
NC C1C C2C C3C
NC C4C C3C C2C
ND C1D C2D C3D
ND C4D C3D C2D
NA C1A CHA C4D
NA C4A CHB C1B
NB C1B CHB C4A
NB C4B CHC C1C
NC C1C CHC C4B
NC C4C CHD C1D
ND C1D CHD C4C
ND C4D CHA C1A
CHA C1A C4D HA
CHB C1B C4A HB
CHC C1C C4B HC
CHD C1D C4C HD
C1A C2A CHA NA
C4A C3A CHB NA
C1B C2B CHB NB
C4B C3B CHC NB
C1C C2C CHC NC
C4C C3C CHD NC
C1D C2D CHD ND
C4D C3D CHA ND
NA C1A C4A FE
NB C1B C4B FE
NC C1C C4C FE
ND C1D C4D FE
...
I also had to edit the .r2b file :
[merged.r2b file]
; rtp residue to rtp building block table
;GMX Force-field
HISD HSD
HIS1 HSD
HISE HSE
HISH HSP
LYSN LSN
ASPH ASPP
GLUH GLUP
RA ADE
RG GUA
RU URA
RC CYT
HEM HEME
Hope it can help,
Cheers,
Florent
On 07/06/16 20:41, Carla Perez wrote:
> Dear all,
>
>
> I am trying to set up a MD simulation using the AMBER03 forcefield in
> gromacs. I am working with a HEM containing protein and wanted to ask if
> anyone happens to have the itp or top parameters for HEM as there is
> currently no entry in the residue database for AMBER03.
>
>
> Thank you,
>
> Carla
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