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AMBER Archive (2005)
Subject: AMBER: Antechamber/Leap, problem with Improper angles
From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
Date: Mon Nov 14 2005 - 20:06:28 CST
- Previous message: Guanglei Cui: "Re: AMBER: iwork array for nmr"
- Next in thread: David A. Case: "Re: AMBER: Antechamber/Leap, problem with Improper angles"
- Reply: David A. Case: "Re: AMBER: Antechamber/Leap, problem with Improper angles"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Dear Amber list,
I have a problem using antechamber/Leap on some ligands, especially when
it comes to assign improper angles. All the necessary files are attatched.
- When I run antechamber (distribute with amber 8):
"antechamber -nc 0 -rn lig -i tobeconvert.mol2 -fi mol2 -o lig_bcc.prepi
-fo prepi -c bcc -j 4 -at gaff -pf y"
"lig_bcc.prepi" indicated 15 improper angles.
- When I run parmchk:
"parmchk -i lig_bcc.prepi -o lig_bcc.frcmod -f prepi"
"lig_bcc.frcmod" just shows 4 additional dihedral angles ...
when running Leap with the following script:
"source leaprc.gaff
mods = LoadAmberParams lig_bcc.frcmod
LoadAmberPrep lig_bcc.prepi
saveAmberParm lig lig_bcc.prmtop lig_bcc.prmcrd
quit"
"lig_bcc.prmtop" shows 12 improper angles (negative value of the 3th
dihedral angle) instead of 15 as in "lig_bcc.prepi".
the one I particularly miss is "C2 C4 C3 O1" which should be planar.
***So my first question is why 12 improper angles with Leap when
antechamber defined 15.
***My second question is that I am not really sure about how to
interpret the Leap log file "leap.log".
Did Leap find only 1 improper angle only ? why there is 12 improper
angles in "lig_bcc.prmtop" than ?
please have a look at it in the following line from the "leap.log" file.
---------------------------------------------------------------------
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C17 H13 C16 C15
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C16 H14 C17 C12
** Warning: No sp2 improper torsion term for ca-oh-ca-ca
atoms are: C16 O3 C15 C14
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C15 H12 C14 C13
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C14 H11 C13 C12
** Warning: No sp2 improper torsion term for ca-c-ca-ca
atoms are: C13 C11 C12 C17
** Warning: No sp2 improper torsion term for c-cc-cd-ca
atoms are: C11 C3 C4 C5
** Warning: No sp2 improper torsion term for cd-c3-cc-os
atoms are: C4 C2 C3 O1
** Warning: No sp2 improper torsion term for os-ca-ca-ca
atoms are: O1 C5 C10 C9
** Warning: No sp2 improper torsion term for ca-ca-ca-cd
atoms are: C10 C6 C5 C4
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C5 H7 C6 C7
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C6 H8 C7 C8
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C7 H9 C8 C9
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C8 H10 C9 C10
old PREP-specified impropers:
<lig 1>: C17 C15 C16 H13
<lig 1>: C12 C16 C17 H14
<lig 1>: C14 C16 C15 O3
<lig 1>: C13 C15 C14 H12
<lig 1>: C14 C12 C13 H11
<lig 1>: C11 C13 C12 C17
<lig 1>: C12 C4 C11 O2
<lig 1>: C11 C5 C4 C3
<lig 1>: C2 C4 C3 O1
<lig 1>: C5 C9 C10 O1
<lig 1>: C10 C6 C5 C4
<lig 1>: C5 C7 C6 H7
<lig 1>: C6 C8 C7 H8
<lig 1>: C7 C9 C8 H9
<lig 1>: C10 C8 C9 H10
total 1 improper torsion applied
15 improper torsions in old prep form
---------------------------------------------------------------------
Any suggestions ?
Thanks a lot for any help.
Chris
-- -------------------------------------------------------------------------- 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_at_picasso.ucsf.edu http://mondale.ucsf.edu -------------------------------------------------------------------------- In a world without walls and fences, who needs Windows and Gates? - Sun Microsystems
@<TRIPOS>MOLECULE
ZINC00000071
34 36 0 0 0
SMALL
USER_CHARGES
(2-ethylbenzofuran-3-yl)-(4-hydroxyphenyl)-methanone
@<TRIPOS>ATOM
1 C1 3.9785 0.5008 -2.4654 C.3 1 <0> 0.0000
2 C2 3.3916 0.7264 -3.8497 C.3 1 <0> 0.1800
3 C3 1.9178 0.9211 -3.7955 C.2 1 <0> -0.0400
4 C4 0.8272 0.0936 -3.5620 C.2 1 <0> -0.0860
5 C5 -0.3181 0.9530 -3.5545 C.ar 1 <0> 0.0000
6 C6 -1.7031 0.7838 -3.3632 C.ar 1 <0> -0.1500
7 C7 -2.5410 1.9043 -3.4477 C.ar 1 <0> -0.1500
8 C8 -2.0212 3.1718 -3.7181 C.ar 1 <0> -0.1500
9 C9 -0.6506 3.3644 -3.9120 C.ar 1 <0> -0.1500
10 C10 0.1551 2.2308 -3.8201 C.ar 1 <0> 0.1400
11 O1 1.5049 2.2104 -3.9672 O.3 1 <0> -0.2800
12 C11 0.8361 -1.3373 -3.3056 C.2 1 <0> 0.5698
13 O2 0.1153 -1.8482 -2.4536 O.2 1 <0> -0.5700
14 C12 1.7094 -2.2202 -4.1085 C.ar 1 <0> 0.0862
15 C13 1.8225 -2.0519 -5.4937 C.ar 1 <0> -0.1500
16 C14 2.6343 -2.9145 -6.2306 C.ar 1 <0> -0.1500
17 C15 3.3160 -3.9425 -5.5831 C.ar 1 <0> 0.0825
18 C16 3.1944 -4.1265 -4.2067 C.ar 1 <0> -0.1500
19 C17 2.3826 -3.2663 -3.4669 C.ar 1 <0> -0.1500
20 O3 4.1024 -4.7676 -6.3366 O.3 1 <0> -0.5325
21 H1 4.5065 -5.4310 -5.7516 H 1 <0> 0.4500
22 H2 5.0648 0.3818 -2.5295 H 1 <0> 0.0000
23 H3 3.7678 1.3483 -1.8041 H 1 <0> 0.0000
24 H4 3.5672 -0.3997 -1.9975 H 1 <0> 0.0000
25 H5 3.8648 1.6097 -4.2955 H 1 <0> 0.0000
26 H6 3.6461 -0.1151 -4.4997 H 1 <0> 0.0000
27 H7 -2.1242 -0.1955 -3.1550 H 1 <0> 0.1500
28 H8 -3.6114 1.7830 -3.3011 H 1 <0> 0.1500
29 H9 -2.6936 4.0242 -3.7784 H 1 <0> 0.1500
30 H10 -0.2365 4.3437 -4.1201 H 1 <0> 0.1500
31 H11 1.2831 -1.2641 -6.0127 H 1 <0> 0.1500
32 H12 2.7276 -2.7837 -7.3051 H 1 <0> 0.1500
33 H13 3.7207 -4.9314 -3.7020 H 1 <0> 0.1500
34 H14 2.2890 -3.4145 -2.3940 H 1 <0> 0.1500
@<TRIPOS>BOND
1 1 2 1
2 1 22 1
3 1 23 1
4 1 24 1
5 2 3 1
6 2 25 1
7 2 26 1
8 3 11 1
9 3 4 2
10 4 5 1
11 4 12 1
12 5 10 ar
13 5 6 ar
14 6 7 ar
15 6 27 1
16 7 8 ar
17 7 28 1
18 8 9 ar
19 8 29 1
20 9 10 ar
21 9 30 1
22 10 11 1
23 12 13 2
24 12 14 1
25 14 19 ar
26 14 15 ar
27 15 16 ar
28 15 31 1
29 16 17 ar
30 16 32 1
31 17 18 ar
32 17 20 1
33 18 19 ar
34 18 33 1
35 19 34 1
36 20 21 1
remark goes here
MASS
BOND
ANGLE
DIHE
c -cd-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
cd-cc-os-ca 1 1.050 180.000 2.000 same as X -c2-os-X
cc-cd-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
c3-cc-os-ca 1 1.050 180.000 2.000 same as X -c2-os-X
IMPROPER
NONBON
log started: Mon Nov 14 18:03:32 2005
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: /home/chris/prog/amber8/dat/leap/parm/gaff.dat
>
> mods = LoadAmberParams lig_bcc.frcmod
Loading parameters: ./lig_bcc.frcmod
Reading force field mod type file (frcmod)
> LoadAmberPrep lig_bcc.prepi
Loading Prep file: ./lig_bcc.prepi
Loaded UNIT: lig
> saveAmberParm lig lig_bcc.prmtop lig_bcc.prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C17 H13 C16 C15
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C16 H14 C17 C12
** Warning: No sp2 improper torsion term for ca-oh-ca-ca
atoms are: C16 O3 C15 C14
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C15 H12 C14 C13
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C14 H11 C13 C12
** Warning: No sp2 improper torsion term for ca-c-ca-ca
atoms are: C13 C11 C12 C17
** Warning: No sp2 improper torsion term for c-cc-cd-ca
atoms are: C11 C3 C4 C5
** Warning: No sp2 improper torsion term for cd-c3-cc-os
atoms are: C4 C2 C3 O1
** Warning: No sp2 improper torsion term for os-ca-ca-ca
atoms are: O1 C5 C10 C9
** Warning: No sp2 improper torsion term for ca-ca-ca-cd
atoms are: C10 C6 C5 C4
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C5 H7 C6 C7
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C6 H8 C7 C8
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C7 H9 C8 C9
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C8 H10 C9 C10
old PREP-specified impropers:
<lig 1>: C17 C15 C16 H13
<lig 1>: C12 C16 C17 H14
<lig 1>: C14 C16 C15 O3
<lig 1>: C13 C15 C14 H12
<lig 1>: C14 C12 C13 H11
<lig 1>: C11 C13 C12 C17
<lig 1>: C12 C4 C11 O2
<lig 1>: C11 C5 C4 C3
<lig 1>: C2 C4 C3 O1
<lig 1>: C5 C9 C10 O1
<lig 1>: C10 C6 C5 C4
<lig 1>: C5 C7 C6 H7
<lig 1>: C6 C8 C7 H8
<lig 1>: C7 C9 C8 H9
<lig 1>: C10 C8 C9 H10
total 1 improper torsion applied
15 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
> quit
Quit
0 0 2
This is a remark line
molecule.res
lig 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 C16 ca M 3 2 1 1.540 111.208 180.000 -0.22588
5 C17 ca S 4 3 2 1.395 54.460 -139.322 -0.04311
6 H14 ha E 5 4 3 1.087 119.320 106.221 0.15116
7 H13 ha E 4 3 2 1.086 119.033 -32.133 0.13953
8 C15 ca M 4 3 2 1.394 95.022 97.657 0.14609
9 O3 oh S 8 4 3 1.367 120.977 -128.351 -0.49297
10 H1 ho E 9 8 4 0.972 108.611 -0.132 0.42312
11 C14 ca M 8 4 3 1.393 120.943 51.280 -0.17046
12 H12 ha E 11 8 4 1.086 120.389 -179.404 0.15568
13 C13 ca M 11 8 4 1.394 119.668 0.356 -0.06203
14 H11 ha E 13 11 8 1.087 118.993 -178.995 0.14692
15 C12 ca M 13 11 8 1.400 119.748 0.494 -0.20431
16 C11 c M 15 13 11 1.479 120.911 -178.817 0.62128
17 O2 o E 16 15 13 1.228 118.365 135.716 -0.52588
18 C4 cd M 16 15 13 1.454 119.724 -42.812 -0.21504
19 C3 cc M 18 16 15 1.389 127.657 -43.026 0.10325
20 C2 c3 3 19 18 16 1.488 134.935 -1.427 -0.03543
21 C1 c3 3 20 19 18 1.521 111.600 -72.415 -0.09081
22 H2 hc E 21 20 19 1.095 110.147 -178.783 0.04318
23 H3 hc E 21 20 19 1.095 111.195 -59.001 0.04766
24 H4 hc E 21 20 19 1.095 111.444 61.413 0.04373
25 H5 hc E 20 19 18 1.097 109.652 166.935 0.07226
26 H6 hc E 20 19 18 1.093 110.653 50.138 0.07377
27 O1 os M 19 18 16 1.364 110.237 -178.778 -0.19821
28 C10 ca M 27 19 18 1.358 107.575 1.160 0.05162
29 C5 ca M 28 27 19 1.388 110.190 -0.084 -0.07709
30 C6 ca M 29 28 27 1.408 118.130 179.620 -0.07603
31 H7 ha E 30 29 28 1.087 121.010 179.829 0.15527
32 C7 ca M 30 29 28 1.401 118.944 -0.024 -0.14525
33 H8 ha E 32 30 29 1.087 119.442 -179.940 0.13584
34 C8 ca M 32 30 29 1.397 120.972 0.029 -0.11336
35 H9 ha E 34 32 30 1.087 119.441 -179.973 0.13595
36 C9 ca M 34 32 30 1.397 121.112 0.016 -0.12077
37 H10 ha E 36 34 32 1.084 121.748 -179.864 0.15032
LOOP
C12 C17
C5 C4
C9 C10
IMPROPER
C17 C15 C16 H13
C12 C16 C17 H14
C14 C16 C15 O3
C13 C15 C14 H12
C14 C12 C13 H11
C11 C13 C12 C17
C12 C4 C11 O2
C11 C5 C4 C3
C2 C4 C3 O1
C5 C9 C10 O1
C10 C6 C5 C4
C5 C7 C6 H7
C6 C8 C7 H8
C7 C9 C8 H9
C10 C8 C9 H10
DONE
STOP
lig
34
3.5369136 1.4228577 -0.0000019 2.7244204 2.2821900 0.7398817
2.6307249 2.1340411 1.8126548 4.0654800 0.6197728 0.5050410
3.6585922 1.6081159 -1.3762685 4.4461652 0.7835675 -2.1302829
4.8513547 0.1214063 -1.5453489 2.9748936 2.6344610 -2.0240502
3.0686602 2.7646451 -3.0981339 2.1624094 3.4947829 -1.2871976
1.6209976 4.2816417 -1.8061343 2.0486973 3.3265695 0.0980005
1.1738681 4.2081043 0.9011264 0.4535503 3.6955759 1.7534415
1.1621673 5.6393293 0.6450522 2.2517085 6.4684527 0.4110108
3.7262482 6.2762033 0.3570024 4.3128239 6.0522716 1.7423632
5.3996239 5.9353607 1.6773816 4.1011757 6.8990971 2.4035112
3.9034922 5.1504240 2.2094215 4.1976231 7.1611549 -0.0880541
3.9818623 5.4355458 -0.2930786 1.8363784 7.7563818 0.2400268
0.4864832 7.7748571 0.3870153 0.0160193 6.4963874 0.6529531
-1.3683823 6.3248493 0.8439270 -1.7876733 5.3437964 1.0520117
-2.2082317 7.4429861 0.7589331 -3.2781931 7.3199736 0.9059693
-1.6905309 8.7121067 0.4888819 -2.3648660 9.5625430 0.4288870
-0.3208181 8.9066735 0.2948727 0.0922085 9.8870954 0.0869354
%VERSION VERSION_STAMP = V0001.000 DATE = 11/14/05 18:03:32
%FLAG TITLE
%FORMAT(20a4)
lig
%FLAG POINTERS
%FORMAT(10I8)
34 8 14 22 28 31 42 44 0 0
170 1 22 31 44 14 21 10 11 0
0 0 0 0 0 0 0 0 34 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C16 C17 H14 H13 C15 O3 H1 C14 H12 C13 H11 C12 C11 O2 C4 C3 C2 C1 H2 H3
H4 H5 H6 O1 C10 C5 C6 H7 C7 H8 C8 H9 C9 H10
%FLAG CHARGE
%FORMAT(5E16.8)
-4.11605312E+00 -7.85563353E-01 2.75448287E+00 2.54255752E+00 2.66209581E+00
-8.98304723E+00 7.71021958E+00 -3.10617326E+00 2.83684766E+00 -1.13032927E+00
2.67722032E+00 -3.72299811E+00 1.13211505E+01 -9.58274312E+00 -3.91852339E+00
1.88145247E+00 -6.45616089E-01 -1.65476706E+00 7.86838914E-01 8.68474818E-01
7.96861179E-01 1.31674340E+00 1.34425907E+00 -3.61184208E+00 9.40635126E-01
-1.40475711E+00 -1.38544147E+00 2.82937652E+00 -2.64678908E+00 2.47531723E+00
-2.06567993E+00 2.47732168E+00 -2.20070717E+00 2.73917614E+00
%FLAG MASS
%FORMAT(5E16.8)
1.20100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01
1.00800000E+00 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.60000000E+01 1.20100000E+01
1.20100000E+01 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 1 2 2 1 3 4 1 2 1
2 1 1 5 1 1 6 6 7 7
7 7 7 8 1 1 1 2 1 2
1 2 1 2
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
11 11 5 4 7 4 1 5 3 5
2 5 8 3 12 12 9 6 4 3
2 2 1 6 8 7 6 3 5 3
3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 29 2 3
5 8 12 17 23 30 4 5 6 9
13 18 24 31 7 8 9 10 14 19
25 32 11 12 13 14 15 20 26 33
16 17 18 19 20 21 27 34 22 23
24 25 26 27 28 35 29 30 31 32
33 34 35 36
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
lig
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
4.78400000E+02 3.44300000E+02 3.86100000E+02 3.69600000E+02 3.49700000E+02
6.48000000E+02 3.77400000E+02 5.04000000E+02 4.11700000E+02 3.37300000E+02
3.76100000E+02 3.03100000E+02 3.37300000E+02 3.72400000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.38700000E+00 1.08700000E+00 1.36200000E+00 9.74000000E-01 1.48700000E+00
1.21400000E+00 1.46200000E+00 1.37100000E+00 1.43400000E+00 1.49900000E+00
1.37000000E+00 1.53500000E+00 1.09200000E+00 1.37300000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
4.85000000E+01 6.72000000E+01 6.98000000E+01 6.46000000E+01 4.89000000E+01
6.87000000E+01 6.48000000E+01 6.57000000E+01 6.36000000E+01 6.89000000E+01
6.48000000E+01 7.00000000E+01 6.60000000E+01 6.82000000E+01 6.47000000E+01
4.72000000E+01 6.62000000E+01 6.78000000E+01 4.64000000E+01 3.94000000E+01
6.98000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.09457053E+00 2.09387240E+00 2.09334880E+00 2.09683946E+00 1.91061275E+00
2.15443535E+00 1.99124700E+00 2.09299974E+00 2.14588324E+00 2.19405434E+00
2.08479669E+00 2.09963199E+00 2.09614133E+00 1.98112408E+00 1.88670173E+00
1.93487284E+00 1.91584874E+00 2.02266294E+00 1.92073567E+00 1.89106506E+00
2.08043336E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
3.62500000E+00 9.00000000E-01 2.87500000E+00 4.00000000E+00 2.55000000E+00
0.00000000E+00 1.05000000E+00 1.55555556E-01 1.50000000E-01 1.05000000E+01
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
3.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
8.19971662E+05 7.62451550E+04 5.71629601E+03 7.01803794E+05 6.00750218E+04
5.81803229E+05 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
5.74393458E+05 4.77908183E+04 4.71003287E+05 0.00000000E+00 3.79876399E+05
9.24822270E+05 8.59947003E+04 7.91544157E+05 0.00000000E+00 6.47841731E+05
1.04308023E+06 8.61541883E+04 6.55825601E+03 6.82786631E+04 0.00000000E+00
5.44261042E+04 9.71708117E+04 7.51607703E+03 5.57281136E+05 4.68711055E+04
4.58874091E+05 0.00000000E+00 3.70622491E+05 6.28541240E+05 5.33379252E+04
3.61397723E+05
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
5.31102864E+02 1.04660679E+02 1.85196588E+01 6.14502845E+02 1.16187983E+02
6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
5.55666448E+02 1.03580945E+02 6.29300710E+02 0.00000000E+00 5.64885984E+02
5.99015525E+02 1.18043746E+02 6.93079947E+02 0.00000000E+00 6.26720080E+02
6.75612247E+02 1.12529845E+02 2.00642027E+01 1.25287818E+02 0.00000000E+00
1.11805549E+02 1.26919150E+02 2.17257828E+01 5.19163331E+02 9.73010751E+01
5.89183300E+02 0.00000000E+00 5.29252520E+02 5.85549272E+02 1.04986921E+02
4.95732238E+02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 9 2 3 6 2 15 18 4 21
24 2 27 30 2 48 63 13 48 66
13 51 54 13 51 57 13 51 60 13
78 81 2 84 87 2 90 93 2 96
99 2
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 1 0 12 1 3 33 1 12
15 3 12 21 1 21 27 1 27 33
1 33 36 5 36 39 6 36 42 7
42 45 8 42 75 9 45 48 10 45
69 11 48 51 12 69 72 14 72 75
1 72 96 1 75 78 1 78 84 1
84 90 1 90 96 1
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 3 6 1 3 0 9 1 6 3
33 1 9 0 12 1 12 15 18 5
12 21 24 1 21 27 30 1 24 21
27 1 30 27 33 1 45 48 63 16
45 48 66 16 48 51 54 19 48 51
57 19 48 51 60 19 51 48 63 19
51 48 66 19 54 51 57 20 54 51
60 20 57 51 60 20 63 48 66 20
72 96 99 1 75 78 81 1 78 84
87 1 81 78 84 1 84 90 93 1
87 84 90 1 90 96 99 1 93 90
96 1
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 33 2 0 12 15 3 0 12
21 2 3 0 12 2 3 33 27 2
3 33 36 4 12 21 27 2 15 12
21 3 21 27 33 2 27 33 36 4
33 36 39 6 33 36 42 7 36 42
45 8 36 42 75 9 39 36 42 10
42 45 48 11 42 45 69 12 42 75
72 13 42 75 78 13 45 42 75 14
45 48 51 15 45 69 72 17 48 45
69 18 69 72 75 21 69 72 96 21
72 75 78 2 72 96 90 2 75 72
96 2 75 78 84 2 78 84 90 2
84 90 96 2
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
0 12 15 18 2 0 12 21 24 1
3 33 27 30 1 9 0 3 6 1
12 0 3 6 1 6 3 33 27 1
6 3 33 36 1 9 0 3 33 1
9 0 12 15 1 9 0 12 21 1
12 21 27 30 1 15 12 21 24 1
18 15 12 21 2 24 21 27 30 1
24 21 27 33 1 30 27 33 36 1
42 45 48 63 6 42 45 48 66 6
42 75 78 81 1 45 48 51 54 8
45 48 51 57 8 45 48 51 60 8
54 51 48 63 9 54 51 48 66 9
57 51 48 63 9 57 51 48 66 9
60 51 48 63 9 60 51 48 66 9
63 48 45 69 6 66 48 45 69 6
69 72 96 99 1 72 75 78 81 1
72 96 90 93 1 75 72 96 99 1
75 78 84 87 1 78 84 90 93 1
81 78 84 87 1 81 78 84 90 1
84 90 96 99 1 87 84 90 93 1
87 84 90 96 1 93 90 96 99 1
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 33 27 1 0 3 33 36 1
0 12 -21 27 1 3 0 12 15 1
3 0 12 21 1 3 33 -27 21 1
3 33 36 39 1 3 33 36 42 1
12 0 3 33 1 12 21 -27 33 1
15 12 21 27 1 21 27 33 36 1
27 33 36 39 1 27 33 36 42 1
33 36 42 45 3 33 36 42 75 3
36 42 45 48 4 36 42 45 69 4
36 42 75 72 5 36 42 75 78 5
39 36 42 45 3 39 36 42 75 3
42 45 48 51 6 42 45 -69 72 7
42 75 -72 69 1 42 75 72 96 1
42 75 78 84 1 45 42 -75 72 5
45 42 75 78 5 45 69 -72 75 2
45 69 72 96 2 48 45 42 75 4
48 45 69 72 7 51 48 45 69 6
69 45 -42 75 4 69 72 75 78 1
69 72 96 90 1 72 75 78 84 1
72 96 -90 84 1 75 72 96 90 1
75 78 -84 90 1 78 75 72 96 1
78 84 -90 96 1 33 42 -36 -39 10
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 12
13 3 4 5 6 8 10 11 12 13
14 15 4 5 10 12 13 5 6 8
12 6 7 8 9 10 11 12 7 8
9 10 8 9 10 11 12 13 10 11
12 11 12 13 14 15 12 13 13 14
15 16 26 14 15 16 17 24 25 26
27 15 16 26 16 17 18 22 23 24
25 26 27 28 29 33 17 18 19 20
21 22 23 24 25 26 27 33 18 19
20 21 22 23 24 25 26 19 20 21
22 23 24 20 21 22 23 21 22 23
22 23 23 24 24 25 26 27 31 33
34 26 27 28 29 31 32 33 34 27
28 29 30 31 33 34 28 29 30 31
32 33 29 30 31 30 31 32 33 34
31 32 33 32 33 34 33 34 34 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
ca ca ha ha ca oh ho ca ha ca ha ca c o cd cc c3 c3 hc hc
hc hc hc os ca ca ca ha ca ha ca ha ca ha
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E B S E B E S E M M E M B 3 3 E E
E E E E M M B E B E S E M E
%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
%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
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 8.00000000E-01 1.70000000E+00 1.30000000E+00 1.70000000E+00
1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.70000000E+00
1.70000000E+00 1.70000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.50000000E+00 1.70000000E+00
1.70000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 7.20000000E-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
8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01
7.20000000E-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 7.20000000E-01
7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
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