[AMBER] parameter file for modified nucleosides (O6-methyl guanine)

From: N.R. Jena <nrjena.gmail.com>
Date: Tue, 2 Mar 2010 18:23:39 +0530

Thank you very much for your earlier suggestions.

I was trying to build parameter file for 6OG. As a result I created
two files 6OG.prepin and 6OG.frcmod as follows: When I merged these
two files with that of the normal DNA, it worked fine and I created a
new .pdb file (attached) for the whole DNA, where all atoms are
properly connected. To my believe, the new parameters created for 6OG
is alright. I have tested those parameters separately for 6OG and got
proper topology and coordinate files. However, after fusing these
parameters (6OG.prepin and 6OG.frcmod) to that of DNA, though I can
create a untroubled pdb file, I could not save proper .top and .crd
files for the whole DNA.  It would be helpful if the experts can look
this matter again.

There is no error which is:
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: OS - O2
Could not find bond parameter for: CK - P
Building angle parameters.
Could not find angle parameter: OS - O2 - P
Could not find angle parameter: CT - OS - O2
Could not find angle parameter: H5 - CK - P
Could not find angle parameter: CK - P - O2
Could not find angle parameter: CK - P - O2
Could not find angle parameter: CK - P - OS
Could not find angle parameter: NB - CK - P
Could not find angle parameter: N* - CK - P
Building proper torsion parameters.
 ** No torsion terms for OS-O2-P-O2
 ** No torsion terms for OS-O2-P-OS
 ** No torsion terms for CT-OS-O2-P
 ** No torsion terms for H5-CK-P-O2
 ** No torsion terms for H5-CK-P-O2
 ** No torsion terms for H5-CK-P-OS
 ** No torsion terms for NB-CK-P-O2
 ** No torsion terms for NB-CK-P-O2
 ** No torsion terms for NB-CK-P-OS
 ** No torsion terms for N*-CK-P-O2
 ** No torsion terms for N*-CK-P-O2
 ** No torsion terms for N*-CK-P-OS
Building improper torsion parameters.
old PREP-specified impropers:
 <6OG 7>: C4 C8 N9 C1'
 <6OG 7>: C5 N9 C4 N3
 <6OG 7>: N2 N3 C2 N1
 <6OG 7>: C2 H57 N2 H59
 <6OG 7>: C5 N1 C6 O6
 <6OG 7>: C6 C4 C5 N7
 <6OG 7>: H55 N9 C8 N7
 total 630 improper torsions applied
 7 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

----------------------------------------------------------------------------------
6OG.prepin:
 0    0    2

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   O2    M    3   2   1     1.540   111.208   180.000  -0.67994
  5  P        P     M    4   3   2     1.497    63.191  -135.455   1.65389
  6  O2P   O2    E    5   4   3     1.497   119.708    21.487  -0.74993
  7  O5'    OS    M    5   4   3     1.597   109.514   147.148  -0.56407
  8  C5'    CT    M    7   5   4     1.421   119.746  -121.132   0.15040
  9  H69   H1    E    8   7   5     1.000   109.202   -37.427   0.05371
 10  H71   H1    E    8   7   5     1.000   109.222    82.273   0.05632
 11  C4'    CT    M    8   7   5     1.505   110.455  -157.571   0.00178
 12  H73   H1    E   11   8   7     1.000   106.429   164.996   0.07642
 13  C3'    CT    3   11   8   7     1.512   112.078    43.751   0.46443
 14  C2'    CT    B   13  11   8     1.511   102.985   -88.669  -0.18540
 15  H65   HC    E   14  13  11     1.000   111.386    82.647   0.04209
 16  H67   HC    E   14  13  11     1.000   111.400  -154.782   0.06652
 17  H77   H1    E   13  11   8     0.999   114.615    34.033  -0.21841
 18  O3'    O     E   13  11   8     1.429   108.356   154.238  -0.80537
 19  O4'   OS    M   11   8   7     1.437   109.349   -72.096  -0.43210
 20  C1'   CT    M   19  11   8     1.411   110.610   109.014   0.25917
 21  H75   H2    E   20  19  11     1.000   114.970   105.868   0.08474
 22  N9    N*    M   20  19  11     1.457   107.744  -136.937  -0.25646
 23  C4    CB    M   22  20  19     1.364   125.447  -105.290   0.46572
 24  N3    NC    M   23  22  20     1.347   125.709    -0.536  -0.75274
 25  C2    CQ    M   24  23  22     1.311   111.850   179.249   0.86767
 26  N2    N2    B   25  24  23     1.340   119.615  -179.595  -0.90696
 27  H57   H     E   26  25  24     1.000   120.010    -0.035   0.40510
 28  H59   H     E   26  25  24     1.000   120.033  -179.988   0.39807
 29  N1    NC    M   25  24  23     1.412   121.158     0.349  -0.83834
 30  C6    CA    M   29  25  24     1.321   127.514    -0.092   0.72539
 31  O6    OS    S   30  29  25     1.320   120.102   179.622  -0.42295
 32  C     CT    3   31  30  29     1.456   120.252     0.158   0.12456
 33  H49   H1    E   32  31  30     1.000   109.511   179.994   0.05305
 34  H51   H1    E   32  31  30     1.000   109.448   -59.976   0.04078
 35  H53   H1    E   32  31  30     1.000   109.470    59.994   0.03667
 36  C5    CB    M   30  29  25     1.389   111.734    -0.344  -0.19840
 37  N7    NB    M   36  30  29     1.382   130.273  -179.427  -0.54863
 38  C8    CK    M   37  36  30     1.304   104.220   179.991   0.43094
 39  H55   H5    E   38  37  36     1.000   123.508   179.741   0.10228


LOOP
 C1'  C2'
  C8   N9
  C5   C4

IMPROPER
  C4   C8   N9  C1'
  C5   N9   C4   N3
  N2   N3   C2   N1
  C2  H57   N2  H59
  C5   N1   C6   O6
  C6   C4   C5   N7
 H55   N9   C8   N7

DONE
STOP
-----------------------------------------
6OG.frcmod

remark goes here
MASS
O2 16.000        0.434               same as o
P  30.970        1.538               same as p4
OS 16.000        0.465               same as os
CT 12.010        0.878               same as c3
H1 1.008         0.135               same as hc
HC 1.008         0.135               same as hc
O  16.000        0.434               same as o
H2 1.008         0.135               same as hc
N* 14.010        0.530               same as na
CB 12.010        0.360               same as c2
NC 14.010        0.530               same as n2
CQ 12.010        0.360               same as c2
N2 14.010        0.530               same as n3
H  1.008         0.161               same as hn
CA 12.010        0.360               same as c2
NB 14.010        0.530               same as n2
CK 12.010        0.360               same as c2
H5 1.008         0.135               same as ha

BOND
O2-P   456.40   1.503       same as o -p4
P -OS  311.60   1.636       same as os-p4
OS-CT  301.50   1.439       same as c3-os
CT-H1  337.30   1.092       same as c3-hc
CT-CT  303.10   1.535       same as c3-c3
CT-O   422.60   1.335       same as c3-o
CT-HC  337.30   1.092       same as c3-hc
CT-H2  337.30   1.092       same as c3-hc
CT-N*  334.70   1.456       same as c3-na
N*-CB  411.10   1.391       same as c2-na
N*-CK  411.10   1.391       same as c2-na
CB-NC  431.60   1.376       same as cc-nc
CB-CB  418.30   1.429       same as cc-cc
NC-CQ  431.60   1.376       same as cc-nc
CQ-N2  449.00   1.364       same as cc-nh
N2-H   394.10   1.018       same as hn-n3
NC-CA  492.90   1.336       same as ca-nc
CA-OS  392.60   1.357       same as c2-os
CA-CB  411.70   1.434       same as ca-cc
CB-NB  431.60   1.376       same as cc-nc
NB-CK  431.60   1.376       same as cc-nc
CK-H5  344.30   1.087       same as c2-ha

ANGLE
O2-P -O2   45.100     117.220   same as o -p4-o
O2-P -OS   43.100     116.670   same as o -p4-os
P -OS-CT   77.600     117.480   same as c3-os-p4
OS-CT-H1   50.900     108.700   same as hc-c3-os
OS-CT-CT   67.800     108.420   same as c3-c3-os
CT-CT-H1   46.400     110.050   same as c3-c3-hc
CT-CT-CT   63.200     110.630   same as c3-c3-c3
H1-CT-H1   39.400     108.350   same as hc-c3-hc
CT-CT-O    62.686     116.465   Calculated with empirical approach
CT-OS-CT   62.100     113.410   same as c3-os-c3
CT-CT-HC   46.400     110.050   same as c3-c3-hc
CT-CT-H2   46.400     110.050   same as c3-c3-hc
CT-CT-N*   65.800     112.590   same as c3-c3-na
HC-CT-HC   39.400     108.350   same as hc-c3-hc
H1-CT-O    47.523     115.325   Calculated with empirical approach
OS-CT-H2   50.900     108.700   same as hc-c3-os
OS-CT-N*   71.200     109.190   same as na-c3-os
CT-N*-CB   64.200     117.200   same as c2-na-c3
CT-N*-CK   64.200     117.200   same as c2-na-c3
H2-CT-N*   49.900     109.500   same as hc-c3-na
N*-CB-NC   71.700     123.620   same as n2-c2-na
N*-CB-CB   69.800     121.380   same as c2-c2-na
N*-CK-NB   71.700     123.620   same as n2-c2-na
N*-CK-H5   51.200     112.420   same as ha-c2-na
CB-N*-CK   67.800     110.370   same as c2-na-c2
CB-NC-CQ   68.600     110.190   same as cc-nc-cc
CB-CB-CA   67.700     111.040   same as ca-cc-cc
CB-CB-NB   70.000     113.420   same as cc-cc-nc
NC-CB-CB   70.000     113.420   same as cc-cc-nc
NC-CQ-N2   73.900     111.940   same as nc-cc-nh
NC-CQ-NC   68.100     123.870   same as ne-ce-ne
CQ-N2-H    49.100     119.380   same as c2-n3-hn
CQ-NC-CA   69.426     110.070   Calculated with empirical approach
CQ-NC-CA   68.600     110.190   same as cc-nc-cc
H -N2-H    41.300     107.130   same as hn-n3-hn
NC-CA-OS   74.600     118.960   same as n2-c2-os
NC-CA-CB   70.000     113.420   same as cc-cc-nc
CA-OS-CT   64.200     112.090   same as c2-os-c3
CA-CB-NB   70.000     113.420   same as cc-cc-nc
OS-CA-CB   71.200     121.430   same as c2-c2-os
CB-NB-CK   68.600     110.190   same as cc-nc-cc
NB-CK-H5   52.400     120.540   same as ha-c2-n2

DIHE
O2-P -OS-CT   1    1.050       180.000           2.000      same as X -os-p4-X
P -OS-CT-H1   1    0.383         0.000           3.000      same as X -c3-os-X
P -OS-CT-CT   1    0.383         0.000           3.000      same as X -c3-os-X
OS-CT-CT-H1   1    0.156         0.000           3.000      same as X -c3-c3-X
OS-CT-CT-CT   1    0.156         0.000           3.000      same as X -c3-c3-X
OS-CT-CT-OS   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-CT-CT   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-CT-H1   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-CT-O    1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-OS-CT   1    0.383         0.000           3.000      same as X -c3-os-X
H1-CT-CT-H1   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-CT-HC   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-OS-CT-H2   1    0.383         0.000           3.000      same as X -c3-os-X
CT-OS-CT-N*   1    0.383         0.000           3.000      same as X -c3-os-X
H1-CT-CT-O    1    0.156         0.000           3.000      same as X -c3-c3-X
H1-CT-OS-CT   1    0.383         0.000           3.000      same as X -c3-os-X
CT-CT-CT-H2   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-CT-N*   1    0.156         0.000           3.000      same as X -c3-c3-X
CT-CT-N*-CB   1    0.000         0.000           2.000      same as X -c3-na-X
CT-CT-N*-CK   1    0.000         0.000           2.000      same as X -c3-na-X
HC-CT-CT-H1   1    0.156         0.000           3.000      same as X -c3-c3-X
HC-CT-CT-O    1    0.156         0.000           3.000      same as X -c3-c3-X
HC-CT-CT-OS   1    0.156         0.000           3.000      same as X -c3-c3-X
HC-CT-CT-H2   1    0.156         0.000           3.000      same as X -c3-c3-X
HC-CT-CT-N*   1    0.156         0.000           3.000      same as X -c3-c3-X
O -CT-CT-OS   1    0.156         0.000           3.000      same as X -c3-c3-X
OS-CT-N*-CB   1    0.000         0.000           2.000      same as X -c3-na-X
OS-CT-N*-CK   1    0.000         0.000           2.000      same as X -c3-na-X
CT-N*-CB-NC   1    0.625       180.000           2.000      same as X -c2-na-X
CT-N*-CB-CB   1    0.625       180.000           2.000      same as X -c2-na-X
CT-N*-CK-NB   1    0.625       180.000           2.000      same as X -c2-na-X
CT-N*-CK-H5   1    0.625       180.000           2.000      same as X -c2-na-X
H2-CT-N*-CB   1    0.000         0.000           2.000      same as X -c3-na-X
H2-CT-N*-CK   1    0.000         0.000           2.000      same as X -c3-na-X
N*-CB-NC-CQ   1    4.150       180.000           2.000      same as X -c2-n2-X
N*-CB-CB-CA   1    6.650       180.000           2.000      same as X -c2-c2-X
N*-CB-CB-NB   1    6.650       180.000           2.000      same as X -c2-c2-X
N*-CK-NB-CB   1    4.150       180.000           2.000      same as X -c2-n2-X
CB-N*-CK-NB   1    0.625       180.000           2.000      same as X -c2-na-X
CB-N*-CK-H5   1    0.625       180.000           2.000      same as X -c2-na-X
CB-NC-CQ-N2   1    4.750       180.000           2.000      same as X -cc-nc-X
CB-NC-CQ-NC   1    4.750       180.000           2.000      same as X -cc-nc-X
CB-CB-CA-NC   1    4.000       180.000           2.000      same as X -cc-cc-X
CB-CB-CA-OS   1    6.650       180.000           2.000      same as X -c2-c2-X
CB-CB-NB-CK   1    4.750       180.000           2.000      same as X -cc-nc-X
NC-CB-N*-CK   1    0.625       180.000           2.000      same as X -c2-na-X
NC-CB-CB-CA   1    4.000       180.000           2.000      same as X -cc-cc-X
NC-CB-CB-NB   1    4.000       180.000           2.000      same as X -cc-cc-X
NC-CQ-N2-H    1    0.300       180.000           2.000      same as X -c2-n3-X
NC-CQ-NC-CA   1    4.750       180.000           2.000      same as X -cc-nc-X
CQ-NC-CB-CB   1    4.750       180.000           2.000      same as X -cc-nc-X
CQ-NC-CA-OS   1    4.150       180.000           2.000      same as X -c2-n2-X
CQ-NC-CA-CB   1    4.800       180.000           2.000      same as X -ca-nc-X
N2-CQ-NC-CA   1    4.750       180.000           2.000      same as X -cc-nc-X
NC-CA-OS-CT   1    1.050       180.000           2.000      same as X -c2-os-X
NC-CA-CB-NB   1    4.000       180.000           2.000      same as X -cc-cc-X
CA-OS-CT-H1   1    0.383         0.000           3.000      same as X -c3-os-X
CA-CB-NB-CK   1    4.750       180.000           2.000      same as X -cc-nc-X
OS-CA-CB-NB   1    6.650       180.000           2.000      same as X -c2-c2-X
CT-OS-CA-CB   1    1.050       180.000           2.000      same as X -c2-os-X
CB-CB-N*-CK   1    0.625       180.000           2.000      same as X -c2-na-X
CB-NB-CK-H5   1    4.750       180.000           2.000      same as X -cc-nc-X

IMPROPER
CB-CK-N*-CT         1.1          180.0         2.0          Using default value
CB-N*-CB-NC         1.1          180.0         2.0          Using default value
N2-NC-CQ-NC         1.1          180.0         2.0          Using default value
CQ-H -N2-H             1.1          180.0         2.0          Using
default value
CB-NC-CA-OS         1.1          180.0         2.0          Using default value
CA-CB-CB-NB         1.1          180.0         2.0          Using default value
H5-N*-CK-NB           1.1          180.0         2.0          Using
default value

NONBON
 O2          1.6612  0.2100             same as o
 P           2.1000  0.2000             same as p4
 OS          1.6837  0.1700             same as os
 CT          1.9080  0.1094             same as c3
 H1          1.4870  0.0157             same as hc
 HC          1.4870  0.0157             same as hc
 O           1.6612  0.2100             same as o
 H2          1.4870  0.0157             same as hc
 N*          1.8240  0.1700             same as na
 CB          1.9080  0.0860             same as cc
 NC          1.8240  0.1700             same as nc
 CQ          1.9080  0.0860             same as cc
 N2          1.8240  0.1700             same as nh
 H           0.6000  0.0157             same as hn
 CA          1.9080  0.0860             same as ca
 NB          1.8240  0.1700             same as nc
 CK          1.9080  0.0860             same as cc
 H5          1.4870  0.0157             same as hc


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Received on Tue Mar 02 2010 - 05:00:03 PST
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