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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- chemical/x-pdb attachment: 11.pdb
Received on Tue Mar 02 2010 - 05:00:03 PST
