Thank you very much. Using RED III.4, and changing the atom names in the
mol2 file to match the atom names in the PDB file, fixed the problem.
You are right that the order of the atom names did not matter.
Andrea Millen
-----Original Message-----
From: FyD [mailto:fyd.q4md-forcefieldtools.org]
Sent: Friday, September 10, 2010 12:46 AM
To: amber.ambermd.org
Cc: q4md-fft.q4md-forcefieldtools.org
Subject: Re: [AMBER] Building a sequence using a new molecular fragment
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 Mon Sep 20 2010 - 11:30:05 PDT
