Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 1 Feb 2010 06:53:36 -0500

it looks to me like your problem is that you used lower case atom types.
since normal DNA is upper case types, you need all of the terms
defined for the connection between your mod G and the other DNA.
you will have to be very careful doing this- and also make SURE to
duplicate the dihedral terms for DNA in your frcmod. you haven't done
this, which means that your G backbone and glycosidic angle will not
behave correctly. you want to make sure that differences between the
mod G and real G are from the O6-me, not from things that you didn't
put in properly.
to summarize, what I mean is that even if you don't get errors I think
this looks incorrect.


On Mon, Feb 1, 2010 at 6:47 AM, N.R. Jena <nrjena.gmail.com> wrote:
> Dear All,
> I have a non standard residue where guanine has been modified to
> O6-methylguanine. I have treated it in antechamber and created 1.prepin and
> 1.frcmod files as follows. However, while uploading all these files along
> with the original .pdb file in .tleap, it is unable to save the final .top
> and .crd files. I guess there is somewhere connectivity problem but unable
> to trace it. It will be extremely helpful if someone can trace the problem
> and help to solve this.
>
> PS: While saving the .top file it is asking for some strange parameters (!)
> as given below (extreme last).
>
> With regards,
> -N R Jena.
>
> 1.prepin:
> -----------------------------------------------------------------------
> This is a remark line
> molecule.res
> 6OG    INT  0
> CORRECT     OMIT DU   BEG
>  0.0000
>   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
>   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
>   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
>   4  O1P   o     M    3   2   1     1.540   111.208   180.000  -0.67935
>   5  P     p4    M    4   3   2     1.497    63.191  -135.455   1.65250
>   6  O2P   o     E    5   4   3     1.497   119.708    21.487  -0.74911
>   7  O5'   os    M    5   4   3     1.597   109.514   147.148  -0.56330
>   8  C5'   c3    M    7   5   4     1.421   119.746  -121.132   0.15117
>   9  H69   h1    E    8   7   5     1.000   109.202   -37.427   0.05306
>  10  H71   h1    E    8   7   5     1.000   109.222    82.273   0.05662
>  11  C4'   c3    M    8   7   5     1.505   110.455  -157.571   0.00155
>  12  C3'   c3    3   11   8   7     1.512   112.078    43.751   0.46165
>  13  C2'   c3    B   12  11   8     1.511   102.985   -88.669  -0.18552
>  14  H65   hc    E   13  12  11     1.000   111.386    82.647   0.04195
>  15  H67   hc    E   13  12  11     1.000   111.400  -154.782   0.06635
>  16  O3'   o     E   12  11   8     1.403   108.374   154.249  -0.80798
>  17  H77   h1    E   12  11   8     0.999   114.615    34.033  -0.21291
>  18  H73   h1    E   11   8   7     1.000   106.429   164.996   0.07584
>  19  O4'   os    M   11   8   7     1.437   109.349   -72.096  -0.43132
>  20  C1'   c3    M   19  11   8     1.411   110.610   109.014   0.25931
>  21  H75   h2    E   20  19  11     1.000   114.970   105.868   0.08448
>  22  N9    na    M   20  19  11     1.457   107.744  -136.937  -0.25723
>  23  C4    ca    M   22  20  19     1.364   125.447  -105.290   0.46631
>  24  N3    nb    M   23  22  20     1.347   125.709    -0.536  -0.75225
>  25  C2    ca    M   24  23  22     1.311   111.850   179.249   0.86736
>  26  N2    nh    B   25  24  23     1.340   119.615  -179.595  -0.90689
>  27  H57   hn    E   26  25  24     1.000   109.483    59.993   0.39800
>  28  H59   hn    E   26  25  24     1.000   109.506   -59.991   0.40479
>  29  N1    nb    M   25  24  23     1.370   123.482     0.358  -0.83893
>  30  C6    ca    M   29  25  24     1.391   125.193    -0.104   0.72532
>  31  O6    os    S   30  29  25     1.349   120.111   179.623  -0.42270
>  32  C     c3    3   31  30  29     1.426   120.207     0.154   0.12447
>  33  H49   h1    E   32  31  30     1.000   109.472   179.992   0.05312
>  34  H51   h1    E   32  31  30     1.000   109.481    60.009   0.03628
>  35  H53   h1    E   32  31  30     1.000   109.476   -59.984   0.04086
>  36  C5    ca    M   30  29  25     1.389   111.731    -0.335  -0.19892
>  37  N7    nc    M   36  30  29     1.382   130.273  -179.431  -0.54803
>  38  C8    cd    M   37  36  30     1.304   104.220   179.991   0.43144
>  39  H55   h5    E   38  37  36     1.000   123.508   179.741   0.10202
> LOOP
>  C1'  C2'
>   C8   N9
>   C5   C4
>
> IMPROPER
>  C1'   C4   N9   C8
>   C5   N9   C4   N3
>   N3   N1   C2   N2
>   C2  H57   N2  H59
>   C5   N1   C6   O6
>   C4   C6   C5   N7
>  H55   N9   C8   N7
>
> DONE
> STOP
>
> 1.frcmod
> -----------------------------------------------------------------------------
> remark goes here
> MASS
>
> BOND
>
> ANGLE
> c3-c3-o    62.686     116.465   Calculated with empirical approach
> nb-ca-os   72.377     119.785   Calculated with empirical approach
>
> DIHE
>
> IMPROPER
> c3-ca-na-cd         1.1          180.0         2.0          Using default
> value
> ca-na-ca-nb         1.1          180.0         2.0          Using default
> value
> nb-nb-ca-nh         1.1          180.0         2.0          Using default
> value
> ca-hn-nh-hn         1.1          180.0         2.0          Using default
> value
> ca-nb-ca-os         1.1          180.0         2.0          Using default
> value
> ca-ca-ca-nc         1.1          180.0         2.0          Using default
> value
> h5-na-cd-nc         1.1          180.0         2.0          Using default
> value
>
> NONBON
>
> --------------------------------------------------------------
> Error in .tleap
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: OS - o
> Could not find bond parameter for: cd - P
> Building angle parameters.
> Could not find angle parameter: OS - o - p4
> Could not find angle parameter: CT - OS - o
> Could not find angle parameter: h5 - cd - P
> Could not find angle parameter: cd - P - O2
> Could not find angle parameter: cd - P - O2
> Could not find angle parameter: cd - P - OS
> Could not find angle parameter: nc - cd - P
> Could not find angle parameter: na - cd - P
> Building proper torsion parameters.
>  ** No torsion terms for  OS-o-p4-o
>  ** No torsion terms for  OS-o-p4-os
>  ** No torsion terms for  CT-OS-o-p4
>  ** No torsion terms for  h5-cd-P-O2
>  ** No torsion terms for  h5-cd-P-O2
>  ** No torsion terms for  h5-cd-P-OS
>  ** No torsion terms for  nc-cd-P-O2
>  ** No torsion terms for  nc-cd-P-O2
>  ** No torsion terms for  nc-cd-P-OS
>  ** No torsion terms for  na-cd-P-O2
>  ** No torsion terms for  na-cd-P-O2
>  ** No torsion terms for  na-cd-P-OS
> Building improper torsion parameters.
> old PREP-specified impropers:
>  <6OG 7>:  C1'  C4   N9   C8
>  <6OG 7>:  C5   N9   C4   N3
>  <6OG 7>:  N3   N1   C2   N2
>  <6OG 7>:  C2   H57  N2   H59
>  <6OG 7>:  C5   N1   C6   O6
>  <6OG 7>:  C4   C6   C5   N7
>  <6OG 7>:  H55  N9   C8   N7
>  total 610 improper torsions applied
>  7 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved.
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>

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Received on Mon Feb 01 2010 - 04:00:04 PST
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