Sorry for not being more explicit Dac.
Yes this is true that my initial pdb is not exactly "standatly" formated
pdb, nevertheless antechamber/tleap reads it without warning (I could
see) and the final pdb has some mistake in some atoms type.
I am using antechamber 1.25 and tleap (Amber 8)
Here are my commands:
antechamber -nc -5 -rn lig -i liga_regul.pdb -fi pdb -o lig_bcc.mol2 -fo
mol2 -c bcc -j 4 -at gaff -pf y
parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod
leap.inp is the following:
verbosity 1
source leaprc.gaff
mods = LoadAmberParams lig_bcc.frcmod
LIG = loadMol2 lig_bcc.mol2
saveAmberParm LIG lig_bcc.prmtop lig_bcc.prmcrd
savePdb LIG liga_leap.pdb
quit
Now follow some of the H atom type like "HN22" in my original pdb file
"liga_regul.pdb" line 9.
This atom type name is correctly defined in "lig_bcc.mol2" (output of
Antechamber) line 15.
the problem is in "liga_leap.pdb" (output of Tleap) , there is no atom
type "HN22" anymore but it is called "2HN2" line 7
Why I say its a bug ?, if you look at "lig_bcc.prmtop" line 13, it is
define as "HN22" instead of "2HN2" as defined in the "liga_leap.pdb"
pdb file.
Thanks
Chris
David A. Case wrote:
>On Thu, Jun 29, 2006, Christophe Guilbert wrote:
>
>
>
>>Here is small bug that I found when you try to write a pdb file using tleap
>>in amber 8.0 the bug concerns some formatting problem when the pdb file
>>contain 4 letters atom name. when you run a ligand (see attachment ) with
>>antechamber -> parmcheck -> tleap , tleap does not write the pdb file
>>correctly , atom which has 4 characters names (in this example) are not
>>interpreted correctly and named differently in the pdb file by tleap.
>>
>>
>
>I don't see any bug. You don't say what the output from tleap was, or what
>you thought the error was.
>
>Note that the liga_regul.pdb file you used as input does not conform to pdb
>standards, which state that the two character element name must be
>right-justified in columns 13-14. Antechamber still reads it OK, but when
>tleap writes out the pdb file, it follows the Brookhaven standard.
>
>Thus, if you have "HN21" in columns 13-16 of your pdb file, tleap correctly
>translates this to "1HN2" as required by pdb syntax.
>
>If you want to keep the original names, you can use ambpdb with the -aatm
>flag -- see the ambpdb section of the manual (p. 284 for Amber 9) for a fuller
>discussion of atom names in pdb files.
>
>....regards...dac
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
>
--
--------------------------------------------------------------------------
Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
600 16th Street, Suite # S-126-D
San Francisco, CA 94143-2180
for UPS/Fed Ex/DHL, change the zip code of 94107 for physical deliveries of package
Office : 415-476-0707
Office fax : 415-476-0688
Email: cguilbert.picasso.ucsf.edu
http://mondale.ucsf.edu
--------------------------------------------------------------------------
In a world without walls and fences,
who needs Windows and Gates?
- Sun Microsystems
verbosity 1
source leaprc.gaff
mods = LoadAmberParams lig_bcc.frcmod
LIG = loadMol2 lig_bcc.mol2
saveAmberParm LIG lig_bcc.prmtop lig_bcc.prmcrd
savePdb LIG liga_leap.pdb
quit
log started: Wed Jul 5 16:22:17 2006
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /data/warhol/share/antechamber-1.25/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
>
> mods = LoadAmberParams lig_bcc.frcmod
Loading parameters: ./lig_bcc.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> LIG = loadMol2 lig_bcc.mol2
Loading Mol2 file: ./lig_bcc.mol2
Reading MOLECULE named lig
> saveAmberParm LIG lig_bcc.prmtop lig_bcc.prmcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -5.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
lig 1
)
(no restraints)
> savePdb LIG liga_leap.pdb
Writing pdb file: liga_leap.pdb
> quit
Quit
log started: Wed Jul 5 16:31:36 2006
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /data/warhol/share/antechamber-1.25/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
>
> mods = LoadAmberParams lig_bcc.frcmod
Loading parameters: ./lig_bcc.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> LIG = loadMol2 lig_bcc.mol2
Loading Mol2 file: ./lig_bcc.mol2
Reading MOLECULE named lig
> saveAmberParm LIG lig_bcc.prmtop lig_bcc.prmcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -5.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
lig 1
)
(no restraints)
> savePdb LIG liga_leap.pdb
Writing pdb file: liga_leap.pdb
> quit
Quit
-I: Adding /data/warhol/share/antechamber-1.25/dat/leap/prep to search path.
-I: Adding /data/warhol/share/antechamber-1.25/dat/leap/lib to search path.
-I: Adding /data/warhol/share/antechamber-1.25/dat/leap/parm to search path.
-I: Adding /data/warhol/share/antechamber-1.25/dat/leap/cmd to search path.
-f: Source leap.inp.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leap.inp
----- Source: /data/warhol/share/antechamber-1.25/dat/leap/cmd/leaprc.gaff
----- Source of /data/warhol/share/antechamber-1.25/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /data/warhol/share/antechamber-1.25/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
Loading parameters: ./lig_bcc.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./lig_bcc.mol2
Reading MOLECULE named lig
Checking Unit.
WARNING: The unperturbed charge of the unit: -5.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
lig 1
)
(no restraints)
Writing pdb file: liga_leap.pdb
Quit
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON
.<TRIPOS>MOLECULE
lig
92 95 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C1 1.9800 -0.8790 43.9990 c3 1 lig 0.4593
2 O1 1.7640 -2.2970 44.2130 os 1 lig -0.5178
3 C2 3.3160 -0.4070 44.6850 c3 1 lig -0.6210
4 N2 4.4410 -1.3420 44.5370 n4 1 lig -1.1753
5 H6 4.6350 -1.4880 43.5580 hn 1 lig 0.3529
6 HN21 5.2560 -0.9820 45.0110 hn 1 lig 0.3165
7 HN22 4.2260 -2.2170 44.9920 hn 1 lig 0.3395
8 H2 3.6040 0.5590 44.2330 hx 1 lig 0.0507
9 C3 3.1310 -0.1920 46.1990 c3 1 lig 0.2895
10 O3 4.2580 0.4810 46.7560 oh 1 lig -0.6568
11 HO3 4.2980 1.3360 46.3200 ho 1 lig 0.3737
12 H3 3.0440 -1.1880 46.6490 h1 1 lig -0.0074
13 C4 1.8580 0.6170 46.4900 c3 1 lig 0.1075
14 O4 1.7270 0.8430 47.8900 oh 1 lig -0.6774
15 HO4 1.6440 -0.0260 48.2910 ho 1 lig 0.4363
16 H4 1.9660 1.5640 45.9450 h1 1 lig 0.0139
17 C5 0.6180 -0.0770 45.8840 c3 1 lig 0.0695
18 C6 -0.6990 0.6520 46.1450 c3 1 lig 0.2965
19 O6 -1.0350 0.6300 47.5260 oh 1 lig -1.0617
20 HO6 -1.1060 -0.2970 47.7670 ho 1 lig 0.3305
21 H61 -1.5030 0.1790 45.5550 h1 1 lig -0.1059
22 H62 -0.6390 1.6910 45.7970 h1 1 lig -0.1179
23 H5 0.5190 -1.1120 46.2440 h1 1 lig 0.0105
24 O5 0.8220 -0.1270 44.4560 os 1 lig -0.4666
25 H1 2.0090 -0.6590 42.9210 h2 1 lig 0.0388
26 C7 0.2340 -5.6030 41.9910 c3 1 lig 0.1414
27 N1 -0.5220 -6.5150 41.1210 n4 1 lig -1.1116
28 H8 -0.9790 -7.2190 41.6790 hn 1 lig -0.7952
29 HN11 -1.1980 -5.9960 40.5790 hn 1 lig 0.3486
30 HN12 0.0970 -6.9430 40.4460 hn 1 lig 0.3557
31 C10 1.0020 -4.5150 41.1810 c3 1 lig 0.1249
32 O2 1.9150 -5.1240 40.2710 oh 1 lig -0.5978
33 HO2 2.5300 -5.6270 40.8100 ho 1 lig 0.3864
34 H11 0.2770 -3.9180 40.5900 h1 1 lig 0.0985
35 C13 1.8040 -3.5700 42.1230 c3 1 lig 0.1007
36 O8 2.3580 -2.4800 41.3280 os 1 lig -0.4166
37 H14 2.6090 -4.1660 42.5970 h1 1 lig 0.0407
38 C16 0.9110 -2.9800 43.2630 c3 1 lig 0.1179
39 H17 0.1840 -2.2740 42.8090 h1 1 lig 0.0581
40 C19 0.1050 -4.0760 44.0310 c3 1 lig 0.1508
41 N5 -0.7980 -3.4840 45.0280 n4 1 lig -1.0991
42 H7 -1.2870 -4.2140 45.5220 hn 1 lig 0.0529
43 HN51 -0.2740 -2.9080 45.6720 hn 1 lig 0.3792
44 HN52 -1.4510 -2.8600 44.5770 hn 1 lig 0.3348
45 H24 0.8170 -4.7280 44.5730 hx 1 lig 0.0384
46 C22 -0.7100 -4.9490 43.0420 c3 1 lig -0.0708
47 H20 -1.3020 -5.7250 43.5610 hc 1 lig 0.0387
48 H22 -1.4760 -4.3040 42.5710 hc 1 lig 0.0445
49 H26 0.9750 -6.2230 42.5320 hx 1 lig 0.0027
50 C8 3.8050 -2.2640 41.2910 c3 1 lig 0.2878
51 C11 4.2580 -2.2090 39.8200 c3 1 lig 0.0584
52 O13 5.6280 -2.5790 39.6920 oh 1 lig -0.5711
53 H29 5.6790 -3.5010 39.9530 ho 1 lig 0.3826
54 H12 3.6380 -2.8450 39.1610 h1 1 lig 0.0517
55 C14 4.0320 -0.7130 39.5540 c3 1 lig 0.1513
56 H15 2.9320 -0.5430 39.5340 h1 1 lig 0.0798
57 C17 4.5760 -0.0720 40.8200 c3 1 lig 0.0749
58 C20 4.0650 1.3460 41.1060 c3 1 lig 0.1340
59 O11 4.6930 1.8650 42.2690 oh 1 lig -0.6385
60 HO5 5.6270 1.6710 42.1730 ho 1 lig 0.4024
61 H51 2.9660 1.3560 41.2380 h1 1 lig 0.0425
62 H52 4.2900 2.0060 40.2510 h1 1 lig 0.1105
63 H18 5.6840 -0.0650 40.8010 h1 1 lig 0.0574
64 O9 4.1310 -0.9690 41.8260 os 1 lig -0.4185
65 H27 4.3300 -3.0100 41.9160 h2 1 lig 0.0850
66 C9 2.4950 2.6990 36.0170 c3 1 lig 0.0924
67 O7 3.2120 3.8370 36.4920 oh 1 lig -0.6607
68 HO1 3.8940 3.4960 37.0750 ho 1 lig 0.4202
69 C12 3.4670 1.7620 35.2470 c3 1 lig 0.2890
70 O14 2.6960 0.8460 34.4730 oh 1 lig -0.7286
71 H30 2.1340 1.3830 33.9110 ho 1 lig 0.3809
72 H13 4.0350 2.3850 34.5380 h1 1 lig -0.0229
73 C15 4.4640 0.9520 36.1390 c3 1 lig -0.6325
74 N3 5.6540 1.7610 36.4390 n4 1 lig -1.1932
75 H10 5.3880 2.5760 36.9690 hn 1 lig 0.3671
76 HN31 6.3290 1.2080 36.9490 hn 1 lig 0.3348
77 HN32 6.1160 2.0290 35.5820 hn 1 lig 0.3216
78 H16 4.7830 0.0660 35.5660 hx 1 lig 0.0547
79 C18 3.7780 0.3970 37.4150 c3 1 lig 0.4752
80 O10 4.6970 -0.1750 38.3780 os 1 lig -0.4101
81 H19 3.1620 -0.4470 37.0960 h2 1 lig -0.0718
82 O12 2.9390 1.4290 38.0350 os 1 lig -0.5073
83 C21 1.8580 1.9320 37.2030 c3 1 lig 0.3138
84 C23 0.8710 2.7750 38.0320 c3 1 lig -0.6700
85 N6 0.2440 2.0090 39.1190 n4 1 lig -1.1865
86 H9 0.9530 1.6620 39.7450 hn 1 lig 0.3649
87 HN61 -0.2980 1.2470 38.7370 hn 1 lig 0.3389
88 HN62 -0.4170 2.5900 39.6150 hn 1 lig 0.3099
89 H21 1.3950 3.6450 38.4550 hx 1 lig 0.0163
90 H23 0.0770 3.1830 37.3800 hx 1 lig -0.0041
91 H25 1.2890 1.0780 36.7890 h1 1 lig -0.0768
92 H28 1.7040 3.0540 35.3310 h1 1 lig -0.0070
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 24 1
4 1 25 1
5 2 38 1
6 3 4 1
7 3 8 1
8 3 9 1
9 4 5 1
10 4 6 1
11 4 7 1
12 9 10 1
13 9 12 1
14 9 13 1
15 10 11 1
16 13 14 1
17 13 16 1
18 13 17 1
19 14 15 1
20 17 18 1
21 17 23 1
22 17 24 1
23 18 19 1
24 18 21 1
25 18 22 1
26 19 20 1
27 26 27 1
28 26 31 1
29 26 46 1
30 26 49 1
31 27 28 1
32 27 29 1
33 27 30 1
34 31 32 1
35 31 34 1
36 31 35 1
37 32 33 1
38 35 36 1
39 35 37 1
40 35 38 1
41 36 50 1
42 38 39 1
43 38 40 1
44 40 41 1
45 40 45 1
46 40 46 1
47 41 42 1
48 41 43 1
49 41 44 1
50 46 47 1
51 46 48 1
52 50 51 1
53 50 64 1
54 50 65 1
55 51 52 1
56 51 54 1
57 51 55 1
58 52 53 1
59 55 56 1
60 55 57 1
61 55 80 1
62 57 58 1
63 57 63 1
64 57 64 1
65 58 59 1
66 58 61 1
67 58 62 1
68 59 60 1
69 66 67 1
70 66 69 1
71 66 83 1
72 66 92 1
73 67 68 1
74 69 70 1
75 69 72 1
76 69 73 1
77 70 71 1
78 73 74 1
79 73 78 1
80 73 79 1
81 74 75 1
82 74 76 1
83 74 77 1
84 79 80 1
85 79 81 1
86 79 82 1
87 82 83 1
88 83 84 1
89 83 91 1
90 84 85 1
91 84 89 1
92 84 90 1
93 85 86 1
94 85 87 1
95 85 88 1
.<TRIPOS>SUBSTRUCTURE
1 lig 1 TEMP 0 **** **** 0 ROOT
lig
92
1.9800000 -0.8790000 43.9990000 1.7640000 -2.2970000 44.2130000
3.3160000 -0.4070000 44.6850000 4.4410000 -1.3420000 44.5370000
4.6350000 -1.4880000 43.5580000 5.2560000 -0.9820000 45.0110000
4.2260000 -2.2170000 44.9920000 3.6040000 0.5590000 44.2330000
3.1310000 -0.1920000 46.1990000 4.2580000 0.4810000 46.7560000
4.2980000 1.3360000 46.3200000 3.0440000 -1.1880000 46.6490000
1.8580000 0.6170000 46.4900000 1.7270000 0.8430000 47.8900000
1.6440000 -0.0260000 48.2910000 1.9660000 1.5640000 45.9450000
0.6180000 -0.0770000 45.8840000 -0.6990000 0.6520000 46.1450000
-1.0350000 0.6300000 47.5260000 -1.1060000 -0.2970000 47.7670000
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6 0 69 48 1 6 0 -69 48 2
6 24 36 39 4 6 24 -36 48 5
6 24 -36 48 6 6 24 -36 48 7
69 0 6 9 4 9 6 24 27 4
9 6 24 36 4 69 0 6 24 4
24 36 48 51 5 24 36 -48 51 6
24 36 -48 51 7 24 36 -48 69 4
27 24 36 39 11 27 24 -36 39 12
27 24 36 48 4 36 48 51 54 4
39 36 48 51 4 39 36 48 69 11
39 36 -48 69 12 54 51 48 69 11
54 51 -48 69 12 69 0 3 111 8
69 0 -3 111 9 69 0 -3 111 10
75 90 102 105 4 75 90 102 111 5
75 90 -102 111 6 75 90 -102 111 7
75 135 -117 111 5 75 135 -117 111 6
75 135 -117 111 7 75 135 117 120 4
78 75 90 93 4 78 75 90 102 4
78 75 135 117 4 90 75 135 117 5
90 75 -135 117 6 90 75 -135 117 7
90 102 105 147 1 90 102 -105 147 2
90 102 -111 117 5 90 102 -111 117 6
90 102 -111 117 7 93 90 75 135 4
93 90 102 105 11 93 90 -102 105 12
93 90 102 111 4 102 90 75 135 5
102 90 -75 135 6 102 90 -75 135 7
102 105 147 150 1 102 105 -147 150 2
102 105 147 189 8 102 105 -147 189 9
102 105 -147 189 10 102 111 117 120 4
102 111 -117 135 5 102 111 -117 135 6
102 111 -117 135 7 105 102 111 117 4
105 147 150 153 11 105 147 -150 153 12
105 147 150 162 4 105 147 189 168 8
105 147 -189 168 9 105 147 -189 168 10
111 102 105 147 1 111 102 -105 147 2
147 150 -162 168 5 147 150 -162 168 6
147 150 -162 168 7 147 150 162 237 4
147 189 -168 162 1 147 189 -168 162 2
147 189 168 171 1 147 189 -168 171 2
150 147 -189 168 1 150 147 -189 168 2
150 162 168 171 5 150 162 -168 171 6
150 162 -168 171 7 150 162 -168 189 4
150 162 237 234 1 150 162 -237 234 2
153 150 147 189 11 153 150 -147 189 12
153 150 162 168 4 153 150 162 237 11
153 150 -162 237 12 162 150 -147 189 4
162 168 171 174 4 162 237 234 216 1
162 237 -234 216 2 162 237 234 243 8
162 237 -234 243 9 162 237 -234 243 10
168 162 237 234 1 168 162 -237 234 2
171 168 162 237 4 174 171 168 189 11
174 171 -168 189 12 189 168 162 237 11
189 168 -162 237 12 195 204 216 219 4
195 204 216 234 5 195 204 -216 234 6
195 204 -216 234 7 195 246 -243 234 1
195 246 -243 234 2 195 246 249 252 4
198 195 204 207 11 198 195 -204 207 12
198 195 204 216 4 198 195 246 243 11
198 195 -246 243 12 198 195 246 249 4
204 195 246 243 4 204 195 246 249 5
204 195 -246 249 6 204 195 -246 249 7
204 216 234 237 4 204 216 -234 243 4
207 204 195 246 4 207 204 216 219 4
207 204 216 234 4 216 204 195 246 5
216 204 -195 246 6 216 204 -195 246 7
216 234 -243 246 1 216 234 -243 246 2
219 216 234 237 4 219 216 234 243 4
234 243 246 249 1 234 243 -246 249 2
237 234 243 246 8 237 234 -243 246 9
237 234 -243 246 10 243 246 249 252 4
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 12
13 17 18 23 24 25 35 38 39 40
3 4 8 9 17 24 25 31 35 36
37 38 39 40 41 45 46 4 5 6
7 8 9 10 11 12 13 14 16 17
24 25 38 5 6 7 8 9 10 12
13 24 25 6 7 8 9 7 8 9
8 9 9 10 12 13 24 25 10 11
12 13 14 15 16 17 18 23 24 25
11 12 13 14 16 17 12 13 13 14
16 17 14 15 16 17 18 19 21 22
23 24 15 16 17 18 23 24 16 17
17 18 23 24 18 19 20 21 22 23
24 25 19 20 21 22 23 24 20 21
22 23 24 21 22 22 23 24 23 24
24 25 38 38 27 28 29 30 31 32
33 34 35 36 37 38 40 41 45 46
47 48 49 28 29 30 31 32 34 35
40 46 47 48 49 29 30 31 46 49
30 31 46 49 31 46 49 32 33 34
35 36 37 38 39 40 46 47 48 49
50 33 34 35 36 37 38 46 49 34
35 35 36 37 38 46 49 36 37 38
39 40 41 45 46 49 50 51 64 65
37 38 39 40 50 51 52 54 55 57
64 65 38 39 40 50 39 40 41 42
43 44 45 46 47 48 50 40 41 45
46 41 42 43 44 45 46 47 48 49
42 43 44 45 46 47 48 43 44 45
46 44 45 46 45 46 46 47 48 47
48 49 48 49 49 0 51 52 53 54
55 56 57 58 63 64 65 80 52 53
54 55 56 57 58 63 64 65 79 80
53 54 55 56 57 64 65 80 54 55
55 56 57 64 65 80 56 57 58 59
61 62 63 64 65 73 79 80 81 82
57 58 63 64 79 80 58 59 60 61
62 63 64 65 79 80 59 60 61 62
63 64 80 60 61 62 63 64 61 62
62 63 64 63 64 64 80 65 80 0
67 68 69 70 71 72 73 74 78 79
82 83 84 85 89 90 91 92 68 69
70 72 73 82 83 84 91 92 69 83
92 70 71 72 73 74 75 76 77 78
79 80 81 82 83 84 91 92 71 72
73 74 78 79 83 92 72 73 73 74
78 79 83 92 74 75 76 77 78 79
80 81 82 83 92 75 76 77 78 79
80 81 82 76 77 78 79 77 78 79
78 79 79 80 81 82 80 81 82 83
84 91 81 82 83 82 83 83 84 85
89 90 91 92 84 85 86 87 88 89
90 91 92 85 86 87 88 89 90 91
92 86 87 88 89 90 91 87 88 89
90 88 89 90 89 90 90 91 91 92
0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
c3 os c3 n4 hn hn hn hx c3 oh ho h1 c3 oh ho h1 c3 c3 oh ho
h1 h1 h1 os h2 c3 n4 hn hn hn c3 oh ho h1 c3 os h1 c3 h1 c3
n4 hn hn hn hx c3 hc hc hx c3 c3 oh ho h1 c3 h1 c3 c3 oh ho
h1 h1 h1 os h2 c3 oh ho c3 oh ho h1 c3 n4 hn hn hn hx c3 os
h2 os c3 c3 n4 hn hn hn hx hx h1 h1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.50000000E+00 1.70000000E+00 1.55000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.50000000E+00
8.00000000E-01 1.30000000E+00 1.70000000E+00 1.50000000E+00 8.00000000E-01
1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 8.00000000E-01
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.50000000E+00 1.30000000E+00
1.70000000E+00 1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.50000000E+00 8.00000000E-01 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00
1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.70000000E+00 1.50000000E+00 8.00000000E-01 1.30000000E+00 1.70000000E+00
1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 8.00000000E-01
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.50000000E+00 1.30000000E+00
1.70000000E+00 1.50000000E+00 8.00000000E-01 1.70000000E+00 1.50000000E+00
8.00000000E-01 1.30000000E+00 1.70000000E+00 1.55000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.50000000E+00
1.30000000E+00 1.50000000E+00 1.70000000E+00 1.70000000E+00 1.55000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 8.50000000E-01 7.20000000E-01 7.90000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01
7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 7.90000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 7.90000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01
-----------------------------------------------------------------------
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Received on Sun Jul 09 2006 - 06:07:10 PDT
