Dear Andrea,
1) I just looked at the mol2 file you generated using R.E.D.
You did not use the last version of the R.E.D.-III.x Tools.
You generated a fragment with a "ugly" set of Cartesian coordinates.
See
http://q4md-forcefieldtools.org/Tutorial/leap.php#4
See Figure 3a (obtained with III.3) versus Figure 3b (obtained with III.4)
If you update to III.4 and set the "Re_fit" mode to "On" in III.4, you
will not recompute the MEP but only re-fit the charges and re-generate
the FF lib (with a correct set of Cart. coordinates) in 5 sec.
This bad set of Cart. coordinates is not a problem when one wants to
create a FF lib. However, this is can be inconvenient in particular if
you do not know the conformation of your polymer and you use the FF
lib (and not the PDB file) as a source of Cartesian coordinates.
2) A limitation of the mol2 file format versus the OFF file format is
that the mol2 file format can not contain information about head &
tail. Consequently, you added these pieces of information using LEaP
commands. This is correct.
3) Your association between R.E.D. to compute the charges, and
Antechamber to assign atom types & find missing FF parameters for the
Cornell et al. FF is... excellent.
You also generated a frcmod files with Antechanber; just check that
the impropers you added in the frcmod are really needed...
4) I do not think the atom order in the FF lib need to match that in
the PDB file. The FF lib and PDB files ONLY need to have identical
_atom names_ and identical _residue name_. Did you carefully check
that ?
If I look at your atom names in the mol2 file generated by R.E.D.,
they look like chemical elements. In the concept of a FF lib two atoms
cannot share the same name in the same residue. Then, I do not
understand how these chemical elements "become" real atom names...
I would update to III.4, set the "Re_fit" mode to "on" and carefully
check manually the atom names in the PDB file used to generate the P2N
file using Ante_R.E.D.
Ante_R.E.D.
PDB -----> P2N
R.E.D.
P2N -----> mol2
With the new version of Ante_R.E.D. 2.0, all these problems of atom
names/residue name are automatically corrected. Ante_R.E.D. 2.0 will
be interfaced by R.E.D. Server 2.0; available soon. Working on it...
I hope this helps.
regards, Francois
Quoting "Millen, Andrea" <andrea.millen.uleth.ca>:
> 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,
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Received on Fri Sep 10 2010 - 00:00:04 PDT
