I noticed my prepin file is ending at C4 (last line). When I load it
in xleap, the connection between other atoms of same residue (residue
7) is excellent. However, if I load this prepin file in tleap, instead
of making a bond between O3' (residue 7) and P atom of another residue
(residue 8) of DNA, tleap is making a bond between C4 (res 7) - P (res
8). Although I specify proper parameters (bond, angle dihedral etc) in
the frcmod file for O3'-P bond, this problem still persists.
Then I tried to rewrite the prepin file where the last line ends at
O3', there is a connectivity problem between the rest of the atoms of
the same residue (res7). Can anyone suggest what should be the proper
prepin file for this modified nucleotide?
Original Prepin ending at C4.
-------------------------------------------
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 -0.67948
5 P P M 4 3 2 1.497 63.191 -135.455 1.65316
6 O2P O2 E 5 4 3 1.497 119.708 21.487 -0.74975
7 O5' OS M 5 4 3 1.597 109.514 147.148 -0.56395
8 C5' CT M 7 5 4 1.421 119.746 -121.132 0.14949
9 H5'1 H1 E 8 7 5 1.000 109.202 -37.427 0.05374
10 H5'2 H1 E 8 7 5 1.000 109.222 82.273 0.05660
11 C4' CT M 8 7 5 1.505 110.455 -157.571 0.00131
12 H4' H1 E 11 8 7 1.000 106.429 164.996 0.07674
13 C3' CT 3 11 8 7 1.512 112.078 43.751 0.46389
14 H3' H1 E 13 11 8 0.999 114.615 34.033 -0.21595
15 C2' CT B 13 11 8 1.511 102.985 -88.669 -0.18546
16 H2'1 HC E 15 13 11 1.000 111.386 82.647 0.04157
17 H2'2 HC E 15 13 11 1.000 111.400 -154.782 0.06642
18 O3' OS E 13 11 8 1.429 108.356 154.238 -0.80589
19 O4' OS M 11 8 7 1.437 109.349 -72.096 -0.43163
20 C1' CT M 19 11 8 1.411 110.610 109.014 0.25911
21 H1' H2 E 20 19 11 1.000 114.970 105.868 0.08524
22 N9 N* M 20 19 11 1.457 107.744 -136.937 -0.25667
23 C8 CK M 22 20 19 1.369 128.030 73.871 0.43041
24 H8 H5 E 23 22 20 1.000 123.507 1.070 0.10238
25 N7 NB M 23 22 20 1.304 112.985 -178.907 -0.54858
26 C5 CB M 25 23 22 1.382 104.220 -0.282 -0.19903
27 C6 CA M 26 25 23 1.389 130.273 179.991 0.72574
28 O6 OS S 27 26 25 1.320 128.163 0.611 -0.42294
29 C CT 3 28 27 26 1.456 120.252 -179.883 0.12454
30 H48 H1 E 29 28 27 1.000 109.511 179.994 0.05303
31 H49 H1 E 29 28 27 1.000 109.448 -59.976 0.04082
32 H50 H1 E 29 28 27 1.000 109.470 59.994 0.03636
33 N1 NC M 27 26 25 1.321 111.734 -179.427 -0.83917
34 C2 CQ M 33 27 26 1.412 127.514 -0.344 0.86872
35 N2 N2 B 34 33 27 1.340 119.227 179.852 -0.90850
36 H21 H E 35 34 33 1.000 120.010 -179.980 0.40587
37 H22 H E 35 34 33 1.000 120.033 0.067 0.39880
38 N3 NC M 34 33 27 1.311 121.158 -0.092 -0.75280
39 C4 CB M 38 34 33 1.347 111.850 0.349 0.46586
LOOP
C1' C2'
C4 N9
C4 C5
IMPROPER
C4 C8 N9 C1'
H8 N9 C8 N7
C6 C4 C5 N7
C5 N1 C6 O6
N2 N1 C2 N3
C2 H21 N2 H22
C5 N9 C4 N3
DONE
------------------------------------------------------
modified prepin ending at O3
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 -0.67948
5 P P M 4 3 2 1.497 63.191 -135.455 1.65316
6 O2P O2 E 5 4 3 1.497 119.708 21.487 -0.74975
7 O5' OS M 5 4 3 1.597 109.514 147.148 -0.56395
8 C5' CT M 7 5 4 1.421 119.746 -121.132 0.14949
9 H5'1 H1 E 8 7 5 1.000 109.202 -37.427 0.05374
10 H5'2 H1 E 8 7 5 1.000 109.222 82.273 0.05660
11 C4' CT M 8 7 5 1.505 110.455 -157.571 0.00131
12 H4' H1 E 11 8 7 1.000 106.429 164.996 0.07674
13 O4' OS M 11 8 7 1.437 109.349 -72.096 -0.43163
14 C1' CT M 13 11 8 1.411 110.610 109.014 0.25911
15 H1' H2 E 14 13 11 1.000 114.970 105.868 0.08524
16 N9 N* M 14 13 11 1.457 107.744 -136.937 -0.25667
17 C8 CK M 16 14 13 1.369 128.030 73.871 0.43041
18 H8 H5 E 17 16 14 1.000 123.507 1.070 0.10238
19 N7 NB M 17 16 14 1.304 112.985 -178.907 -0.54858
20 C5 CB M 19 17 16 1.382 104.220 -0.282 -0.19903
21 C6 CA M 20 19 17 1.389 130.273 179.991 0.72574
22 O6 OS S 21 20 19 1.320 128.163 0.611 -0.42294
23 C CT 3 22 21 20 1.456 120.252 -179.883 0.12454
24 H48 H1 E 23 22 21 1.000 109.511 179.994 0.05303
25 H49 H1 E 23 22 21 1.000 109.448 -59.976 0.04082
26 H50 H1 E 23 22 21 1.000 109.470 59.994 0.03636
27 N1 NC M 21 20 19 1.321 111.734 -179.427 -0.83917
28 C2 CQ M 27 21 20 1.412 127.514 -0.344 0.86872
29 N2 N2 B 28 27 21 1.340 119.227 179.852 -0.90850
30 H21 H E 29 28 27 1.000 120.010 -179.980 0.40587
31 H22 H E 29 28 27 1.000 120.033 0.067 0.39880
32 N3 NC M 28 27 21 1.311 121.158 -0.092 -0.75280
33 C4 CB M 32 28 27 1.347 111.850 0.349 0.46586
34 C3' CT 3 11 8 7 1.512 112.078 43.751 0.46389
35 H3' H1 E 34 11 8 0.999 114.615 34.033 -0.21595
36 C2' CT B 34 11 8 1.511 102.985 -88.669 -0.18546
37 H2'1 HC E 36 34 11 1.000 111.386 82.647 0.04157
38 H2'2 HC E 36 34 11 1.000 111.400 -154.782 0.06642
39 O3' OS E 34 11 8 1.429 108.356 154.238 -0.80589
LOOP
C1' C2'
C4 N9
C4 C5
IMPROPER
C4 C8 N9 C1'
H8 N9 C8 N7
C6 C4 C5 N7
C5 N1 C6 O6
N2 N1 C2 N3
C2 H21 N2 H22
C5 N9 C4 N3
DONE
STOP
On Wed, Mar 3, 2010 at 11:11 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> Even I changed C2 H57 N2 H59 and
>> H55 N9 C8 N7
>> to C2 H21 N2 H22 and
>> H8 N9 C8 N7
>> I got the same error.
>
> I doubt there is an atom type H21 for example. Names and types are
> different and need to be correct. If you 'edit DG', select all atoms,
> and 'edit selected atoms', you will see names and types juxtaposed
> and maybe will be able to map proper types to your own residue.
>
> Note: types will not appear in a pdb, they are only in the ff residue
> template.
>
> Bill
>
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Received on Mon Mar 08 2010 - 23:30:03 PST
