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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Received on Mon Feb 01 2010 - 04:00:02 PST
