Hi,

I am working with a protein that has the HIC residue which needs to built and parametrized.

While searching for the correct parameters, I arrived at this thread. Although, after going through the discussion, I sense that the issue has not been resolved completely.

From what I gather, the correct values are:-

BOND

Code:
NR3-CT3 261.0 1.49
CT3-HA3 322 1.110


ANGLE

Code:
NR3-CT3-HA3 51.5 107.5


DIHEDERALS

Code:
NR3  CPH2 NR3  CT3      1.4000  2   180.00

and
Code:
NR3  CPH2 NR3  CT3      12.0000 2   180.00
HR2  CPH2 NR3  CT3       3.0000 2   180.00
HR1  CPH1 NR3  CT3       0.5000 0     0.00
CPH1 CPH1 NR3  CT3      14.0000 2   180.00

where these values were taken from the protonated histidine. Although the parameters should be kept the same.

IMPROPERS

Code:
NR3  CPH1 CPH2 CT3       1.2000         0      0.0000 ! ALLOW ARO
NR3  CPH2 CPH1 CT3       1.2000         0      0.0000 ! ALLOW ARO

are correct but
Code:
CPH1  NR3  CT3 HA3        0.5000        0       0.0000

is incorrect.

Are these values sufficient and correct?

PS: The topology file can be found below, which I built by attaching the methyl group I found in this discussion to the HSD residue.

Code:

[ HIC ]
 [ atoms ]
        N       NH1     -0.47   0
        HN      H       0.31    1
        CA      CT1     0.07    2
        HA      HB      0.09    3
        CB      CT2     -0.05   4
        HB1     HA      0.09    5
        HB2     HA      0.09    6
        CD2     CPH1    0.19    7
        HD2     HR1     0.13    8
        CG      CPH1    0.19    9
        NE2     NR3     -0.51   10
        CR      CT3     0.17    11
        HR1     HA      0.09    12
        HR2     HA      0.09    13
        HR3     HA      0.09    14
        ND1     NR3     -0.51   15
        HD1     H       0.44    16
        CE1     CPH2    0.32    17
        HE1     HR2     0.18    18
        C       C       0.51    19
        O       O       -0.51   20
 [ bonds ]
        CB      CA
        CG      CB
        ND1     CG
        CE1     ND1
        NE2     CD2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        ND1     HD1
        NE2     CR
        CR      HR1
        CR      HR2
        CR      HR3
        CD2     HD2
        CE1     HE1
        O       C
        CD2     CG
        NE2     CE1
 [ impropers ]
        ND1     CG      CE1     HD1
        CD2     CG      NE2     HD2
        CE1     ND1     NE2     HE1
        NE2     CD2     CE1     CR
        CG      CD2     ND1     CB
        ND1     CE1     CG      HD1
        CD2     NE2     CG      HD2
        CE1     NE2     ND1     HE1
        NE2     CE1     CD2     CR
        CG      ND1     CD2     CB
        N       -C      CA      HN
        C       CA      +N      O
[ cmap ]
        -C      N       CA      C       +N


Any suggestions would be highly appreciated.

I hope this thread could be revived.

Thank you in advance.