Hi,
I am trying to create a library file for a modified base and insert it
into a double helix. I have calculated RESP charges for the guanine
nucleoside using the R.E.D. program and generated the nucleotide
molecular fragment by using inter-molecular charge equivalencing with a
dimethylphosphate group and charge equivalencing between the sugar atoms
of all four nucleosides. Here is the .mol2 file the program created:
.<TRIPOS>MOLECULE
MOL
33 35 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 P -0.000119 -0.614589 0.000001 P 1 MOL
1.1661 ****
2 O 0.967793 0.483511 0.832355 O 1 MOL
-0.4985 ****
3 O 0.825886 -1.299334 -1.045481 O 1 MOL
-0.7680 ****
4 O -0.826433 -1.298291 1.046144 O 1 MOL
-0.7680 ****
5 O -0.968047 0.483060 -0.832917 O 1 MOL
-0.5399 ****
6 C 3.966772 -1.118109 -0.805200 C 1 MOL
-0.0260 ****
7 H 3.729010 -1.572861 -1.776939 H 1 MOL
0.0801 ****
8 H 5.060429 -1.002694 -0.736803 H 1 MOL
0.0801 ****
9 C 3.325816 0.262849 -0.756914 C 1 MOL
0.1980 ****
10 H 3.831728 0.901796 -1.491083 H 1 MOL
0.1024 ****
11 O 1.939458 0.171310 -1.114047 O 1 MOL
-0.4243 ****
12 C 1.104560 0.605981 -0.045218 C 1 MOL
0.1498 ****
13 H 0.692323 1.595291 -0.266570 H 1 MOL
0.1283 ****
14 C 3.378369 0.952263 0.619680 C 1 MOL
0.1141 ****
15 H 4.196199 0.562323 1.239962 H 1 MOL
0.0843 ****
16 C 2.001466 0.628132 1.203252 C 1 MOL
-0.0590 ****
17 H 2.018779 -0.360579 1.668245 H 1 MOL
0.0459 ****
18 H 1.663283 1.361275 1.942717 H 1 MOL
0.0459 ****
19 N -0.034343 -0.287288 0.056035 N 1 MOL
0.0431 ****
20 C -0.012322 -1.670398 0.182936 C 1 MOL
0.0792 ****
21 H 0.928206 -2.202226 0.223814 H 1 MOL
0.1956 ****
22 N -1.205779 -2.204902 0.216646 N 1 MOL
-0.5571 ****
23 C -2.069324 -1.131560 0.102566 C 1 MOL
0.1863 ****
24 C -3.508153 -1.092374 0.090882 C 1 MOL
0.5097 ****
25 O -4.341721 -1.976157 0.186914 O 1 MOL
-0.5468 ****
26 N -3.948027 0.272768 -0.054505 N 1 MOL
-0.5345 ****
27 H -4.954816 0.378242 0.001462 H 1 MOL
0.3601 ****
28 C -3.147600 1.380016 -0.162788 C 1 MOL
0.7094 ****
29 N -3.783006 2.604706 -0.236104 N 1 MOL
-0.8969 ****
30 H -4.652674 2.634454 -0.754273 H 1 MOL
0.3961 ****
31 H -3.145374 3.350073 -0.488209 H 1 MOL
0.3961 ****
32 N -1.837778 1.331042 -0.147977 N 1 MOL
-0.6038 ****
33 C -1.361729 0.065363 -0.005781 C 1 MOL
0.1521 ****
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 6 7 1
5 6 8 1
6 6 9 1
7 9 10 1
8 9 11 1
9 9 14 1
10 11 12 1
11 12 13 1
12 12 16 1
13 12 19 1
14 14 15 1
15 14 16 1
16 16 17 1
17 16 18 1
18 19 20 1
19 19 33 1
20 20 21 1
21 20 22 1
22 22 23 1
23 23 24 1
24 23 33 1
25 24 25 1
26 24 26 1
27 26 27 1
28 26 28 1
29 28 29 1
30 28 32 1
31 29 30 1
32 29 31 1
33 32 33 1
34 2 6 1
35 5 14 1
.<TRIPOS>SUBSTRUCTURE
1 MOL 1 **** 0 **** ****
I then ran antechamber to generate amber atom types, and manually
changed the dangling atoms' types to match the original AMBER paper. I
also ran parmchk to generate the missing parameters. This resulted in a
new mol2 file and a frcmod file:
X.mol2:
.<TRIPOS>MOLECULE
X
33 35 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 P -0.0000 -0.6150 0.0000 P 1 X
1.166100
2 O 0.9680 0.4840 0.8320 OS 1 X
-0.498500
3 O1 0.8260 -1.2990 -1.0450 O2 1 X
-0.768000
4 O2 -0.8260 -1.2980 1.0460 O2 1 X
-0.768000
5 O3 -0.9680 0.4830 -0.8330 OS 1 X
-0.539900
6 C 3.9670 -1.1180 -0.8050 CT 1 X
-0.026000
7 H 3.7290 -1.5730 -1.7770 H1 1 X
0.080100
8 H1 5.0600 -1.0030 -0.7370 H1 1 X
0.080100
9 C1 3.3260 0.2630 -0.7570 CT 1 X
0.198000
10 H2 3.8320 0.9020 -1.4910 H1 1 X
0.102400
11 O4 1.9390 0.1710 -1.1140 OS 1 X
-0.424300
12 C2 1.1050 0.6060 -0.0450 CT 1 X
0.149800
13 H3 0.6920 1.5950 -0.2670 H2 1 X
0.128300
14 C3 3.3780 0.9520 0.6200 CT 1 X
0.114100
15 H4 4.1960 0.5620 1.2400 H1 1 X
0.084300
16 C4 2.0010 0.6280 1.2030 CT 1 X
-0.059000
17 H5 2.0190 -0.3610 1.6680 HC 1 X
0.045900
18 H6 1.6630 1.3610 1.9430 HC 1 X
0.045900
19 N -0.0340 -0.2870 0.0560 N* 1 X
0.043100
20 C5 -0.0120 -1.6700 0.1830 CK 1 X
0.079200
21 H7 0.9280 -2.2020 0.2240 H5 1 X
0.195600
22 N1 -1.2060 -2.2050 0.2170 NB 1 X
-0.557100
23 C6 -2.0690 -1.1320 0.1030 CB 1 X
0.186300
24 C7 -3.5080 -1.0920 0.0910 C 1 X
0.509700
25 O5 -4.3420 -1.9760 0.1870 O 1 X
-0.546800
26 N2 -3.9480 0.2730 -0.0550 NA 1 X
-0.534500
27 H8 -4.9550 0.3780 0.0010 H 1 X
0.360100
28 C8 -3.1480 1.3800 -0.1630 CA 1 X
0.709400
29 N3 -3.7830 2.6050 -0.2360 N2 1 X
-0.896900
30 H9 -4.6530 2.6340 -0.7540 H 1 X
0.396100
31 H10 -3.1450 3.3500 -0.4880 H 1 X
0.396100
32 N4 -1.8380 1.3310 -0.1480 NC 1 X
-0.603800
33 C9 -1.3620 0.0650 -0.0060 CB 1 X
0.152100
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 2
4 6 7 1
5 6 8 1
6 6 9 1
7 9 10 1
8 9 11 1
9 9 14 1
10 11 12 1
11 12 13 1
12 12 16 1
13 12 19 1
14 14 15 1
15 14 16 1
16 16 17 1
17 16 18 1
18 19 20 1
19 19 33 1
20 20 21 1
21 20 22 2
22 22 23 1
23 23 24 ar
24 23 33 ar
25 24 25 2
26 24 26 ar
27 26 27 1
28 26 28 ar
29 28 29 1
30 28 32 ar
31 29 30 1
32 29 31 1
33 32 33 ar
34 2 6 1
35 5 14 1
.<TRIPOS>SUBSTRUCTURE
1 X 1 TEMP 0 **** **** 0 ROOT
X.frcmod:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
H5-N*-CK-NB 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
C -CB-CB-NB 1.1 180.0 2.0 Using
default value
CB-NA-C -O 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
C -CA-NA-H 1.0 180.0 2.0 General
improper torsional angle (2 general atom types)
CB-N*-CB-NC 1.1 180.0 2.0 Using
default value
NONBON
Then, I load the force field in leap, and load the X.frcmod file
(loadamberparams X.frcmod). I load my mol2 file (TEST=loadmol2 X.mol2).
I set my head, tail, and connect atoms:
set TEST head TEST.1.P
set TEST tail TEST.1.O3
set TEST.1 connect0 TEST.1.P
set TEST.1 connect1 TEST.1.O3
set TEST restype nucleic
Then I save this as a library file (saveoff TEST X.lib).
Here is my library file:
!!index array str
"X"
!entry.X.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"P" "P" 0 1 131073 1 15 1.166100
"O" "OS" 0 1 131073 2 8 -0.498500
"O1" "O2" 0 1 131073 3 8 -0.768000
"O2" "O2" 0 1 131073 4 8 -0.768000
"O3" "OS" 0 1 131073 5 8 -0.539900
"C" "CT" 0 1 131073 6 6 -0.026000
"H" "H1" 0 1 131073 7 1 0.080100
"H1" "H1" 0 1 131073 8 1 0.080100
"C1" "CT" 0 1 131073 9 6 0.198000
"H2" "H1" 0 1 131073 10 1 0.102400
"O4" "OS" 0 1 131073 11 8 -0.424300
"C2" "CT" 0 1 131073 12 6 0.149800
"H3" "H2" 0 1 131073 13 1 0.128300
"C3" "CT" 0 1 131073 14 6 0.114100
"H4" "H1" 0 1 131073 15 1 0.084300
"C4" "CT" 0 1 131073 16 6 -0.059000
"H5" "HC" 0 1 131073 17 1 0.045900
"H6" "HC" 0 1 131073 18 1 0.045900
"N" "N*" 0 1 131073 19 7 0.043100
"C5" "CK" 0 1 131073 20 6 0.079200
"H7" "H5" 0 1 131073 21 1 0.195600
"N1" "NB" 0 1 131073 22 7 -0.557100
"C6" "CB" 0 1 131073 23 6 0.186300
"C7" "C" 0 1 131073 24 6 0.509700
"O5" "O" 0 1 131073 25 8 -0.546800
"N2" "NA" 0 1 131073 26 7 -0.534500
"H8" "H" 0 1 131073 27 1 0.360100
"C8" "CA" 0 1 131073 28 6 0.709400
"N3" "N2" 0 1 131073 29 7 -0.896900
"H9" "H" 0 1 131073 30 1 0.396100
"H10" "H" 0 1 131073 31 1 0.396100
"N4" "NC" 0 1 131073 32 7 -0.603800
"C9" "CB" 0 1 131073 33 6 0.152100
!entry.X.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"P" "P" 0 -1 0.0
"O" "OS" 0 -1 0.0
"O1" "O2" 0 -1 0.0
"O2" "O2" 0 -1 0.0
"O3" "OS" 0 -1 0.0
"C" "CT" 0 -1 0.0
"H" "H1" 0 -1 0.0
"H1" "H1" 0 -1 0.0
"C1" "CT" 0 -1 0.0
"H2" "H1" 0 -1 0.0
"O4" "OS" 0 -1 0.0
"C2" "CT" 0 -1 0.0
"H3" "H2" 0 -1 0.0
"C3" "CT" 0 -1 0.0
"H4" "H1" 0 -1 0.0
"C4" "CT" 0 -1 0.0
"H5" "HC" 0 -1 0.0
"H6" "HC" 0 -1 0.0
"N" "N*" 0 -1 0.0
"C5" "CK" 0 -1 0.0
"H7" "H5" 0 -1 0.0
"N1" "NB" 0 -1 0.0
"C6" "CB" 0 -1 0.0
"C7" "C" 0 -1 0.0
"O5" "O" 0 -1 0.0
"N2" "NA" 0 -1 0.0
"H8" "H" 0 -1 0.0
"C8" "CA" 0 -1 0.0
"N3" "N2" 0 -1 0.0
"H9" "H" 0 -1 0.0
"H10" "H" 0 -1 0.0
"N4" "NC" 0 -1 0.0
"C9" "CB" 0 -1 0.0
!entry.X.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.X.unit.childsequence single int
2
!entry.X.unit.connect array int
1
5
!entry.X.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
1 4 2
2 6 1
5 14 1
6 7 1
6 8 1
6 9 1
9 10 1
9 11 1
9 14 1
11 12 1
12 13 1
12 16 1
12 19 1
14 15 1
14 16 1
16 17 1
16 18 1
19 20 1
19 33 1
20 21 1
20 22 2
22 23 1
23 24 4
23 33 4
24 25 2
24 26 4
26 27 1
26 28 4
28 29 1
28 32 4
29 30 1
29 31 1
32 33 4
!entry.X.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
"R" 1 "A" 32
"R" 1 "A" 33
!entry.X.unit.name single str
"X"
!entry.X.unit.positions table dbl x dbl y dbl z
0.716162 -1.257768 0.125583
2.292186 -1.514476 0.332815
0.326065 -1.812634 -1.189684
0.008928 -1.695010 1.350043
3.306971 2.498822 0.273281
3.211340 -1.101407 -0.652622
3.023714 -1.636184 -1.583720
4.225520 -1.308950 -0.310233
3.047557 0.398160 -0.876484
3.780276 0.758529 -1.598739
1.724125 0.656851 -1.307447
0.920307 0.850047 -0.153486
0.488669 1.849853 -0.199243
3.182125 1.106708 0.461587
4.007524 0.713417 1.054421
1.834321 0.760699 1.065434
1.848193 -0.260966 1.445043
1.543429 1.469690 1.840717
-0.165122 -0.145943 -0.066264
-0.089261 -1.486936 0.209168
0.846279 -2.013505 0.327711
-1.250503 -2.073616 0.302011
-2.163816 -1.043671 0.100626
-3.583864 -1.072364 0.114382
-4.326316 -2.034322 0.299592
-4.118708 0.191008 -0.097694
-5.125976 0.266787 -0.092270
-3.382703 1.340378 -0.301480
-4.074001 2.475143 -0.472835
-5.083517 2.461112 -0.447561
-3.584578 3.346551 -0.618062
-2.045667 1.365419 -0.324924
-1.507659 0.140579 -0.116669
!entry.X.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
1 5 0 0 0 0
!entry.X.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"X" 1 34 1 "n" 0
!entry.X.unit.residuesPdbSequenceNumber array int
0
!entry.X.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.X.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
I want to insert the molecular fragment into a sequence of
double-stranded DNA. So I used the nab program to generate the sequence
I want, with G in place of X (which is just G that I have built myself
as a test). I modified the pdb so that where it says sequence 'DG' it
now says 'X'. I also reordered the atoms in the sequence 'X' so it
matches the atom order in the X.mol2 file. Here is a portion of my pdb
file:
ATOM 115 C2 DT 4 2.558 2.202 9.875 1.00 0.00
C
ATOM 116 O2 DT 4 1.738 3.103 9.903 1.00 0.00
O
ATOM 117 C3' DT 4 6.323 5.157 9.475 1.00 0.00
C
ATOM 118 H3' DT 4 7.407 5.127 9.586 1.00 0.00
H
ATOM 119 C2' DT 4 5.688 4.107 10.387 1.00 0.00
C
ATOM 120 H2' DT 4 6.471 3.516 10.862 1.00 0.00
H
ATOM 121 H2'' DT 4 5.093 4.603 11.154 1.00 0.00
H
ATOM 122 O3' DT 4 5.839 6.444 9.833 1.00 0.00
O
ATOM 123 P X 5 5.792 6.854 11.379
1.00 0.00 P
ATOM 124 O5' X 5 4.255 6.582 11.732
1.00 0.00 O
ATOM 125 OP1 X 5 6.090 8.297
11.520 1.00 0.00 O
ATOM 126 OP2 X 5 6.654 5.939
12.161 1.00 0.00 O
ATOM 127 O3' X 5 0.936 8.645 13.213
1.00 0.00 O
ATOM 128 C5' X 5 3.246 6.924 10.764
1.00 0.00 C
ATOM 129 H5' X 5 3.073 6.103 10.068
1.00 0.00 H
ATOM 130 H5'' X 5 3.595 7.798 10.215
1.00 0.00 H
ATOM 131 C4' X 5 1.946 7.263 11.467
1.00 0.00 C
ATOM 132 H4' X 5 1.256 7.809 10.823
1.00 0.00 H
ATOM 133 O4' X 5 1.305 6.011 11.697
1.00 0.00 O
ATOM 134 C1' X 5 1.268 5.671 13.068
1.00 0.00 C
ATOM 135 H1' X 5 0.237 5.620 13.420 1.00 0.00
H
ATOM 136 C3' X 5 2.084 7.888 12.855
1.00 0.00 C
ATOM 137 H3' X 5 2.978 8.501 12.966
1.00 0.00 H
ATOM 138 C2' X 5 2.188 6.666 13.767
1.00 0.00 C
ATOM 139 H2' X 5 3.169 6.649 14.242
1.00 0.00 H
ATOM 140 H2'' X 5 1.415 6.717 14.533
1.00 0.00 H
ATOM 141 N9 X 5 1.738 4.260 13.150
1.00 0.00 N
ATOM 142 C8 X 5 3.025 3.769 13.136
1.00 0.00 C
ATOM 143 H8 X 5 3.861 4.448 13.055
1.00 0.00 N
ATOM 144 N7 X 5 3.098 2.463 13.225
1.00 0.00 C
ATOM 145 C5 X 5 1.766 2.061 13.304
1.00 0.00 H
ATOM 146 C6 X 5 1.21 0.760 13.417
1.00 0.00 N
ATOM 147 O6 X 5 1.787 -0.322 13.473
1.00 0.00 C
ATOM 148 N1 X 5 -0.191 0.806 13.467
1.00 0.00 C
ATOM 149 H1 X 5 -0.677 -0.064 13.549
1.00 0.00 O
ATOM 150 C2 X 5 -0.953 1.956 13.414
1.00 0.00 N
ATOM 151 N2 X 5 -2.275 1.787 13.477
1.00 0.00 H
ATOM 152 H21 X 5 -2.773 0.911 13.547
1.00 0.00 C
ATOM 153 H22 X 5 -2.839 2.623 13.430
1.00 0.00 N
ATOM 154 N3 X 5 -0.429 3.176 13.308
1.00 0.00 H
ATOM 155 C4 X 5 0.928 3.15 13.259
1.00 0.00 H
ATOM 156 P DC 6 0.657 8.949 14.759 1.00 0.00
P
ATOM 157 OP1 DC 6 0.050 10.292 14.900 1.00 0.00
O
ATOM 158 OP2 DC 6 1.892 8.716 15.541 1.00 0.00
O
ATOM 159 O5' DC 6 -0.427 7.826 15.112 1.00 0.00
O
ATOM 160 C5' DC 6 -1.443 7.510 14.144 1.00 0.00
C
ATOM 161 H5' DC 6 -1.100 6.745 13.447 1.00 0.00
H
ATOM 162 H5'' DC 6 -1.674 8.423 13.595 1.00 0.00
H
ATOM 163 C4' DC 6 -2.695 7.020 14.847 1.00 0.00
C
ATOM 164 H4' DC 6 -3.574 7.056 14.204 1.00 0.00
H
ATOM 165 O4' DC 6 -2.477 5.630 15.077 1.00 0.00
O
ATOM 166 C1' DC 6 -2.308 5.333 16.448 1.00 0.00
C
ATOM 167 H1' DC 6 -3.112 4.685 16.798 1.00 0.00
H
ATOM 168 N1 DC 6 -1.098 4.468 16.530 1.00 0.00
N
ATOM 169 C6 DC 6 0.151 5.005 16.501 1.00 0.00
C
ATOM 170 H6 DC 6 0.276 6.074 16.418 1.00 0.00
H
ATOM 171 C5 DC 6 1.254 4.217 16.575 1.00 0.00
C
Now, I load my force field in leap again, and my modified library
(loadoff X.lib). Then, I try to load my pdb with the modified base
(TEST=load pdb nuc.pdb). I get this error:
Loading PDB file: ./nuc.pdb
(starting new molecule for chain .)
(starting new molecule for chain 4)
(starting new molecule for chain 6)
(starting new molecule for chain 0)
(starting new molecule for chain 3)
(starting new molecule for chain 1)
(starting new molecule for chain )
(starting new molecule for chain 2)
(starting new molecule for chain 3)
(starting new molecule for chain 1)
(starting new molecule for chain 3)
(starting new molecule for chain 1)
(starting new molecule for chain 0)
(starting new molecule for chain 2)
(starting new molecule for chain 0)
(starting new molecule for chain )
-- residue 6: duplicate [ X] atoms (total 3)
-- residue 6: duplicate [' X] atoms (total 8)
-- residue 8: duplicate [ X] atoms (total 5)
-- residue 8: duplicate [' X] atoms (total 5)
-- residue 10: duplicate [ X] atoms (total 6)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Unknown residue: 5 number: 4 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: 5 number: 5 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: number: 6 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: 5 number: 7 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: 5 number: 8 type: Nonterminal
Unknown residue: 5 number: 9 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: 5 number: 10 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: 5 sequence: 5
Created a new atom named: X within residue: .R<5 5>
Creating new UNIT for residue: 5 sequence: 6
Created a new atom named: X within residue: .R<5 6>
Created a new atom named: 'X within residue: .R<5 6>
Creating new UNIT for residue: sequence: 7
Created a new atom named: 'X within residue: .R< 7>
Creating new UNIT for residue: 5 sequence: 8
Created a new atom named: 'X within residue: .R<5 8>
Created a new atom named: X within residue: .R<5 8>
Creating new UNIT for residue: 5 sequence: 9
Created a new atom named: X within residue: .R<5 9>
Creating new UNIT for residue: 5 sequence: 10
Created a new atom named: X within residue: .R<5 10>
Created a new atom named: 1X within residue: .R<5 10>
Created a new atom named: 2X within residue: .R<5 10>
Creating new UNIT for residue: 5 sequence: 11
Created a new atom named: X within residue: .R<5 11>
Created a new atom named: P within residue: .R<DC5 12>
Created a new atom named: OP1 within residue: .R<DC5 12>
Created a new atom named: OP2 within residue: .R<DC5 12>
total atoms in file: 632
Leap added 2 missing atoms according to residue templates:
2 H / lone pairs
The file contained 14 atoms not in residue templates
When I open the file in xleap for viewing, there is a gap in the double
helix where X should be. Then there are random unconnected atoms
scattered around the helix. What am I doing wrong? Even the phosphate
atoms of the next nucleotide (DC) are not recognized, although I have
not changed these. Any insight into this problem would be greatly
appreciated. Thank you,
Andrea Millen
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Received on Thu Sep 09 2010 - 17:30:03 PDT
