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AMBER Archive (2003)
Subject: Nmode query
From: kinsellg (kinsellg_at_tcd.ie)
Date: Fri Jan 24 2003 - 09:00:40 CST
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Hi all,
I have created a prmtop and prmcrd for Adrenaline (attached) and was
interested in performing a nmode analysis on it. I took the nmode_min.in and
nmode.in files from the online tutorial but seem to always get the following
error, even though both prmtop and prmcrd seem to have the same number of
atoms. Any ideas where I am going wrong???
Thanks,
Gemma
Binary format used for output coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 01/15/03 Time = 12:54:42
PARM file has the title:
AD
Memory allocation :
1 28 55 66 77
96 115 134 153 172
180 188 196 205 250
295 295 295 295 403
0 1 28 56 84
166 167 170 185 200
215 229 243 257 286
315 344 373 391 409
427 445 917 1389 1861
2333 2805 3277 3749 4221
4693 5165 5300 5327 5410
5466 5494 511 592 754
5522 0 5550 0 0
0 0 0 0 5354
5382 484 0
Duplicated 0 dihedrals
Duplicated 0 dihedrals
Memory allocation :
1 28 55 66 77
96 115 134 153 172
180 188 196 205 250
295 295 295 295 403
0 1 28 56 84
166 167 170 185 200
215 229 243 257 286
315 344 373 391 409
427 445 917 1389 1861
2333 2805 3277 3749 4221
4693 5165 5300 5327 5410
5466 5494 511 592 754
5550 8396 5578 0 0
0 0 0 0 5354
5382 484 0
Total memory required : 8477 real words
Total memory avail : 3500000 real words
Total memory required : 5578 integer words
Total memory avail : 4000000 integer words
Maximum nonbond pairs 3994421
Number of atoms in -p and -c files do not agree!
PRMCRD:
AD
27
4.7176672 4.6558228 3.7269461 5.0440684 5.5727906 4.2131315
3.4317333 4.1784710 3.9519112 2.5357571 4.7936555 4.7777439
2.9875480 5.5307942 5.2219235 2.9960210 3.0068886 3.2930344
1.7210000 2.5905564 3.5409960 1.5836512 1.7406289 3.0941644
3.8665449 2.3542956 2.4247173 3.5303515 1.4590000 1.9059074
5.1556424 2.8477165 2.1907016 5.7863096 2.3471014 1.4590000
5.5955438 4.0016663 2.8437680 6.9802081 4.5871631 2.5877929
6.9935609 6.0027286 2.6697670 6.5117225 6.3579543 1.9065196
7.3307897 4.2468638 1.5989057 8.0420140 4.1881235 3.6338257
8.9671577 4.7399571 3.4487913 7.6925830 4.3975022 4.6470002
8.3767409 2.7178608 3.5758052 7.5025873 2.1781106 3.6338238
8.7822683 2.4995636 2.6545051 9.3447360 2.2515962 4.6438912
8.8934771 2.4307128 5.6197921 10.2719169 2.8174634 4.5418575
9.5377765 1.1876552 4.4988192
11.3719169 7.7237286 6.7197921 90.0000000 90.0000000 90.0000000
PRMTOP:
%VERSION VERSION_STAMP = V0001.000 DATE = 01/15/03 12:54:42
%FLAG TITLE
%FORMAT(20a4)
AD
%FLAG POINTERS
%FORMAT(10I8)
27 9 14 13 28 17 48 23 0
0
134 1 13 17 23 11 19 8 9
0
0 0 0 0 0 0 0 1 27
0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C3 H9 C1 O7 H15 C2 O8 H16 C4 H10 C5 H11 C6 C12 O17 H23 H18 C13 H19
H20
N14 H22 H24 C21 H25 H26 H27
%FLAG CHARGE
%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 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 0.00000000E+00 0.00000000E+00
0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG MASS
%FORMAT(5E16.8)
1.20100000E+01 1.00800000E+00 1.20100000E+01 1.60000000E+01
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
1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00
1.40100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 3 4 1 3 4 1
2
1 2 1 5 3 4 6 5 7
7
8 9 9 5 7 7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
14 6 10 5 1 7 4 1 5
3
6 2 8 10 6 2 4 9 5
4
6 5 4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 29 37
2
3 5 8 12 17 23 30 38 4
5
6 9 13 18 24 31 39 7 8
9
10 14 19 25 32 40 11 12 13
14
15 20 26 33 41 16 17 18 19
20
21 27 34 42 22 23 24 25 26
27
28 35 43 29 30 31 32 33 34
35
36 44 37 38 39 40 41 42 43
44
45
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
AD
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.54500000E+02 4.73700000E+02 3.88700000E+02 5.53200000E+02
3.30300000E+02
3.15000000E+02 3.40400000E+02 3.07600000E+02 3.22700000E+02
2.92700000E+02
3.92200000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.08000000E+00 1.39000000E+00 1.36000000E+00 9.60000000E-01
1.51000000E+00
1.43000000E+00 1.09000000E+00 1.53000000E+00 1.10300000E+00
1.50000000E+00
1.03000000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
7.00000000E+01 6.30000000E+01 6.14000000E+01 4.51000000E+01
4.92000000E+01
6.71220000E+01 4.73000000E+01 6.30000000E+01 4.67000000E+01
4.65000000E+01
8.00000000E+01 5.09000000E+01 6.77000000E+01 4.65000000E+01
5.00000000E+01
6.25000000E+01 3.87000000E+01 4.89000000E+01 3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.09439600E+00 2.09439600E+00 2.13960005E+00 2.14274164E+00
1.89141412E+00
1.93251664E+00 1.90328237E+00 1.98967620E+00 1.90939102E+00
1.91445248E+00
1.94080696E+00 1.91270715E+00 1.91183448E+00 1.92021207E+00
1.91113635E+00
1.94988268E+00 1.92108473E+00 1.88303654E+00 1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
9.00000000E-01 3.62500000E+00 0.00000000E+00 1.66666667E-01
1.55555556E-01
2.50000000E-01 1.60000000E-01 1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00
3.00000000E+00
1.00000000E+00 3.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00
0.00000000E+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
%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
9.24822270E+05 8.59947003E+04 7.91544157E+05 0.00000000E+00
1.04308023E+06
6.01816484E+04 4.33325458E+03 4.66922514E+04 0.00000000E+00
6.78771368E+04
3.25969625E+03 2.01619733E+04 1.21014911E+03 1.45985502E+04
0.00000000E+00
2.27401052E+04 8.79040886E+02 2.01823541E+02 8.82619071E+05
7.91627154E+04
7.44975864E+05 0.00000000E+00 9.95480466E+05 6.20665997E+04
2.01791425E+04
9.44293233E+05 2.27577561E+03 8.90987508E+01 1.40467023E+03
0.00000000E+00
2.56678134E+03 5.94667300E+01 9.14716912E+00 2.12601181E+03
1.39982777E-01
%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
5.99015525E+02 1.18043746E+02 6.93079947E+02 0.00000000E+00
6.75612247E+02
9.40505980E+01 1.63092814E+01 1.03606917E+02 0.00000000E+00
1.06076943E+02
1.43076527E+01 5.44372326E+01 8.61880722E+00 5.79323581E+01
0.00000000E+00
6.13981767E+01 7.42992380E+00 3.56012899E+00 6.53361429E+02
1.26451907E+02
7.50714425E+02 0.00000000E+00 7.36907417E+02 1.13252061E+02
6.45756063E+01
8.01323529E+02 1.82891803E+01 2.33864085E+00 1.79702257E+01
0.00000000E+00
2.06278363E+01 1.93248820E+00 7.57919667E-01 2.09604198E+01
9.37598976E-02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 3 1 9 12 4 18 21 4
24
27 1 30 33 1 39 48 7 42
45
4 51 54 9 51 57 9 60 63
11
60 66 11 69 72 9 69 75 9
69
78 9
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 6 2 0 36 2 6 9 3
6
15 2 15 18 3 15 24 2 24
30
2 30 36 2 36 39 5 39 42
6
39 51 8 51 60 10 60 69 10
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
3 0 6 4 3 0 36 4 6
9
12 5 15 18 21 5 15 24 27
4
24 30 33 4 27 24 30 4 33
30
36 4 36 39 48 7 39 42 45
9
39 51 54 10 39 51 57 10 42
39
48 12 48 39 51 14 51 60 63
15
51 60 66 15 54 51 57 17 54
51
60 18 57 51 60 18 60 69 72
18
60 69 75 18 60 69 78 18 63
60
66 19 63 60 69 15 66 60 69
15
72 69 75 17 72 69 78 17 75
69
78 17
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 6 9 1 0 6 15 2 0
36
30 2 0 36 39 3 6 0 36
2
6 15 18 1 6 15 24 2 9
6
15 1 15 24 30 2 18 15 24
1
24 30 36 2 30 36 39 3 36
39
42 6 36 39 51 8 39 51 60
11
42 39 51 13 51 60 69 16
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
0 6 9 12 1 0 36 30 33
2
0 36 39 48 3 3 0 6 9
2
3 0 6 15 2 3 0 36 30
2
3 0 36 39 2 6 15 18 21
1
6 15 24 27 2 12 9 6 15
1
15 24 30 33 2 18 15 24 27
2
21 18 15 24 1 27 24 30 33
2
27 24 30 36 2 30 36 39 48
3
33 30 36 39 2 36 39 42 45
4
36 39 51 54 5 36 39 51 57
5
39 51 60 63 5 39 51 60 66
5
42 39 51 54 5 42 39 51 57
5
45 42 39 48 4 45 42 39 51
6
45 42 -39 51 7 48 39 51 54
5
48 39 51 57 5 48 39 51 60
5
51 60 69 72 5 51 60 69 75
5
51 60 69 78 5 54 51 60 63
5
54 51 60 66 5 54 51 60 69
5
57 51 60 63 5 57 51 60 66
5
57 51 60 69 5 63 60 69 72
5
63 60 69 75 5 63 60 69 78
5
66 60 69 72 5 66 60 69 75
5
66 60 69 78 5 3 0 -36 -6
8
15 30 -24 -27 8 24 36 -30 -33
8
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 6 15 18 2 0 6 15 24
2
0 36 -30 24 2 0 36 39 42
3
0 36 39 51 3 6 0 36 30
2
6 0 36 39 2 6 15 -24 30
2
36 0 6 9 2 9 6 15 18
2
9 6 15 24 2 36 0 6 15
2
15 24 -30 36 2 18 15 24 30
2
24 30 36 39 2 30 36 39 42
3
30 36 39 51 3 36 39 51 60
5
39 51 60 69 5 42 39 51 60
5
0 15 -6 -9 8 6 24 -15 -18
8
0 30 -36 -39 8
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 9 11 12
13
14 15 17 18 3 4 6 11 13
14
4 5 6 7 8 9 10 11 13
14
5 6 7 9 13 6 7 8 9
10
11 12 13 8 9 10 11 9 10
11
12 13 14 11 12 13 12 13 14
15
17 18 13 14 14 15 16 17 18
19
20 21 15 16 17 18 19 20 21
22
23 24 16 17 18 19 20 21 17
18
18 19 20 21 19 20 21 22 23
24
25 26 27 20 21 22 23 24 21
22
23 24 22 23 24 25 26 27 23
24
25 26 27 24 25 26 27 25 26
27
26 27 27 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 ha ca oh ho ca oh ho ca ha ca ha ca c3 oh ho h1 c3 hx hx
n4 hn hn c3 hx hx hx
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M E B S E B S E B E S E M M S E E M E E
M E E M E E 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
%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
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
1 1 2
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
27
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
9.00000000E+01 1.13719169E+01 7.72372865E+00 6.71979215E+00
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00
1.20000000E+00
1.70000000E+00 1.50000000E+00 1.20000000E+00 1.70000000E+00
1.20000000E+00
1.70000000E+00 1.20000000E+00 1.70000000E+00 1.70000000E+00
1.50000000E+00
1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00
1.20000000E+00
1.55000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.20000000E+00
1.20000000E+00 1.20000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 8.50000000E-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
8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01
7.90000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01
8.50000000E-01 8.50000000E-01
- Next message: caldwell_at_heimdal.compchem.ucsf.edu: "Amber Web page."
- Previous message: Artur Galstyan: "RESP-group constraint"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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