[gmx-users] Small molecule parametrization

[Justin Lemkul]

On 9/7/16 1:43 PM, Sun Iba wrote:
> Hi
> I have parametreized my small molecule with the help of ATB server. I have
> learnt that ATB provides GROMOS charges better than PRODRG. However, I have
> serious doubts regarding the charges assigned to hydrophobic groups. Also I
> need to convert the calculated charges into GROMOS 43a1 set (force field I
> am using). I am pasting the .itp file produced by ATB:
>
> nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
>     1   CH3    1    SCX1    C12    1    0.223  15.0350
>     2    OE    1    SCX1     O1    1   -0.275  15.9994     ; -0.052
>     3     C    1    SCX1     C3    2    0.476  12.0110
>     4     C    1    SCX1     C2    2   -0.157  12.0110
>     5     C    1    SCX1     C4    2   -0.376  12.0110
>     6    HC    1    SCX1     H2    2    0.172   1.0080     ;  0.115
>     7     C    1    SCX1     C6    3    0.095  12.0110
>     8    HC    1    SCX1     H4    3    0.137   1.0080
>     9     C    1    SCX1     C9    3   -0.386  12.0110
>    10     C    1    SCX1    C13    3    0.478  12.0110
>    11    NR    1    SCX1     N2    3   -0.525  14.0067     ; -0.201
>    12     C    1    SCX1    C19    4    0.539  12.0110
>    13    NR    1    SCX1     N4    4   -0.539  14.0067     ;  0.000
>    14     C    1    SCX1     C1    5   -0.117  12.0110
>    15    HC    1    SCX1     H1    5    0.157   1.0080
>    16     C    1    SCX1     C5    5   -0.150  12.0110
>    17    HC    1    SCX1     H3    5    0.131   1.0080     ;  0.021
>    18     C    1    SCX1     C7    6    0.097  12.0110
>    19     C    1    SCX1    C11    6    0.247  12.0110
>    20    HC    1    SCX1     H6    6    0.079   1.0080
>    21    NR    1    SCX1     N1    6   -0.423  14.0067     ;  0.000
>    22    NT    1    SCX1     N3    7    0.171  14.0067
>    23     C    1    SCX1    C16    7    0.387  12.0110
>    24     O    1    SCX1     O2    7   -0.492  15.9994
>    25     C    1    SCX1    C18    7    0.495  12.0110
>    26     F    1    SCX1     F1    7   -0.187  18.9984
>    27     F    1    SCX1     F2    7   -0.187  18.9984
>    28     F    1    SCX1     F3    7   -0.187  18.9984     ;  0.000
>    29     C    1    SCX1    C15    8   -0.211  12.0110
>    30     C    1    SCX1    C14    8    0.388  12.0110
>    31   CH3    1    SCX1    C10    8   -0.060  15.0350     ;  0.117
>    32     C    1    SCX1    C22    9   -0.444  12.0110
>    33    HC    1    SCX1    H11    9    0.187   1.0080
>    34     C    1    SCX1    C21    9    0.309  12.0110
>    35   CH3    1    SCX1     C8    9   -0.052  15.0350     ;  0.000
>    36     C    1    SCX1    C20   10   -0.340  12.0110
>    37    HC    1    SCX1    H10   10    0.226   1.0080
>    38     C    1    SCX1    C17   10   -0.026  12.0110
>    39    HC    1    SCX1     H8   10    0.140   1.0080     ;  0.000
>

What is this molecule and why do you think the charges are inappropriate?

>
> Please have a look and help me understanding if the charges are too bad.
> Also my Nitrogen atom is not aromatic. It is linked to C by triple bond and
> to another N by double bond. Does GROMOS treat this type of nitrogn as NT
> and NR?
>

N can't be linked to one atom via triple bond and another via double bond. 
That's five bonds.  Unless your N has expanded its valence into d-orbitals, 
that's not going to be possible.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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