[gmx-users] Small molecule parametrization

Sun Iba sun.iba2 at gmail.com
Fri Sep 9 14:33:56 CEST 2016


Justin please have look at PDB coordinates:

HEADER    UNCLASSIFIED                            08-Sep-16
TITLE     UNITED ATOM STRUCTURE FOR MOLECULE UNK
AUTHOR    GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2016-09-05 10:31:24
AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
HETATM    1  C12 SCX1    0      -1.450  -4.041  -0.077  1.00  0.00           C
HETATM    2   O1 SCX1    0      -2.719  -3.434  -0.134  1.00  0.00           O
HETATM    3   C3 SCX1    0      -2.815  -2.071  -0.157  1.00  0.00           C
HETATM    4   C2 SCX1    0      -4.079  -1.455  -0.012  1.00  0.00           C
HETATM    5   C4 SCX1    0      -1.693  -1.233  -0.290  1.00  0.00           C
HETATM    6   H2 SCX1    0      -0.689  -1.664  -0.419  1.00  0.00           H
HETATM    7   C6 SCX1    0      -5.387  -2.138   0.065  1.00  0.00           C
HETATM    8   H4 SCX1    0      -6.255  -1.451   0.117  1.00  0.00           H
HETATM    9   C9 SCX1    0      -5.767  -3.438   0.069  1.00  0.00           C
HETATM   10  C13 SCX1    0      -7.246  -3.703   0.131  1.00  0.00           C
HETATM   11   N2 SCX1    0      -8.455  -3.909   0.168  1.00  0.00           N
HETATM   12  C19 SCX1    0      -4.965  -4.688   0.013  1.00  0.00           C
HETATM   13   N4 SCX1    0      -4.368  -5.763  -0.028  1.00  0.00           N
HETATM   14   C1 SCX1    0      -4.139  -0.046   0.045  1.00  0.00           C
HETATM   15   H1 SCX1    0      -5.107   0.471   0.159  1.00  0.00           H
HETATM   16   C5 SCX1    0      -3.004   0.756  -0.044  1.00  0.00           C
HETATM   17   H3 SCX1    0      -3.100   1.853   0.003  1.00  0.00           H
HETATM   18   C7 SCX1    0      -1.760   0.161  -0.251  1.00  0.00           C
HETATM   19  C11 SCX1    0      -0.521   0.988  -0.408  1.00  0.00           C
HETATM   20   H6 SCX1    0      -0.024   1.023  -1.390  1.00  0.00           H
HETATM   21   N1 SCX1    0       0.002   1.677   0.531  1.00  0.00           N
HETATM   22   N3 SCX1    0       1.409   2.643   0.125  1.00  0.00           N
HETATM   23  C16 SCX1    0       1.077   4.001   0.074  1.00  0.00           C
HETATM   24   O2 SCX1    0       1.893   4.908   0.253  1.00  0.00           O
HETATM   25  C18 SCX1    0      -0.392   4.495  -0.144  1.00  0.00           C
HETATM   26   F1 SCX1    0      -0.916   4.834   1.027  1.00  0.00           F
HETATM   27   F2 SCX1    0      -0.433   5.577  -0.910  1.00  0.00           F
HETATM   28   F3 SCX1    0      -1.192   3.601  -0.695  1.00  0.00           F
HETATM   29  C15 SCX1    0       2.780   2.075   0.077  1.00  0.00           C
HETATM   30  C14 SCX1    0       3.094   0.702   0.223  1.00  0.00           C
HETATM   31  C10 SCX1    0       2.068  -0.383   0.443  1.00  0.00           C
HETATM   32  C22 SCX1    0       4.428   0.269   0.163  1.00  0.00           C
HETATM   33  H11 SCX1    0       4.661  -0.804   0.260  1.00  0.00           H
HETATM   34  C21 SCX1    0       5.509   1.132  -0.017  1.00  0.00           C
HETATM   35   C8 SCX1    0       6.926   0.616  -0.050  1.00  0.00           C
HETATM   36  C20 SCX1    0       5.211   2.486  -0.157  1.00  0.00           C
HETATM   37  H10 SCX1    0       6.028   3.213  -0.295  1.00  0.00           H
HETATM   38  C17 SCX1    0       3.887   2.924  -0.131  1.00  0.00           C
HETATM   39   H8 SCX1    0       3.778   4.005  -0.281  1.00  0.00           H
CONECT    1    2
CONECT    2    1    3
CONECT    3    2    4    5
CONECT    4    3    7   14
CONECT    5    3    6   18
CONECT    6    5
CONECT    7    4    8    9
CONECT    8    7
CONECT    9    7   10   12
CONECT   10    9   11
CONECT   11   10
CONECT   12    9   13
CONECT   13   12
CONECT   14    4   15   16
CONECT   15   14
CONECT   16   14   17   18
CONECT   17   16
CONECT   18    5   16   19
CONECT   19   18   20   21
CONECT   20   19
CONECT   21   19   22
CONECT   22   21   23   29
CONECT   23   22   24   25
CONECT   24   23
CONECT   25   23   26   27   28
CONECT   26   25
CONECT   27   25
CONECT   28   25
CONECT   29   22   30   38
CONECT   30   29   31   32
CONECT   31   30
CONECT   32   30   33   34
CONECT   33   32
CONECT   34   32   35   36
CONECT   35   34
CONECT   36   34   37   38
CONECT   37   36
CONECT   38   29   36   39
CONECT   39   38
END



On Fri, Sep 9, 2016 at 5:51 PM, sun.iba2 <sun.iba2 at gmail.com> wrote:

> This is a small molecule with dicyanovinyl group substituted at para
> position on one of the phenyl ring. I suspect the charges are not proper
> because in ATB the group charges must be -1,0 or 1. For some groups charges
> are summed up to zero but this is not the case of all groups.
>
>
> Sent from Samsung Mobile
>
>
> -------- Original message --------
> From: Justin Lemkul <jalemkul at vt.edu>
> Date:09/09/2016 5:18 AM (GMT+05:30)
> To: gmx-users at gromacs.org
> Cc:
> Subject: Re: [gmx-users] Small molecule parametrization
>
>
>
> 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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