I see no redundancies in any of these topologies. All angles, dihedrals, etc.
are unique. Regarding the methane topology, the output of topolgen reproduces
exactly the output of pdb2gmx (if one were to create a methane .rtp entry), so I
don't believe there is any problem with any of these topologies.
-Justin
Víctor Bahamonde wrote:
the coordinates file (created with the free software avogadro) and
topology
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 N1 LIG 1 -6.943 1.034 -0.171 1.00
0.00 N
HETATM 2 C2 LIG 1 -8.112 2.010 -0.344 1.00
0.00 C
HETATM 3 C3 LIG 1 -7.125 0.305 1.155 1.00
0.00 C
HETATM 4 C4 LIG 1 -6.989 0.030 -1.317 1.00
0.00 C
HETATM 5 C5 LIG 1 -5.641 1.857 -0.188 1.00
0.00 C
HETATM 6 C6 LIG 1 -4.374 1.011 -0.060 1.00
0.00 C
HETATM 7 C7 LIG 1 -3.130 1.906 -0.060 1.00
0.00 C
HETATM 8 C8 LIG 1 -1.846 1.078 0.027 1.00
0.00 C
HETATM 9 C9 LIG 1 -0.607 1.975 0.036 1.00
0.00 C
HETATM 10 C10 LIG 1 0.679 1.149 0.079 1.00
0.00 C
HETATM 11 C11 LIG 1 1.916 2.050 0.091 1.00
0.00 C
HETATM 12 C12 LIG 1 3.205 1.227 0.092 1.00
0.00 C
HETATM 13 C13 LIG 1 4.440 2.130 0.107 1.00
0.00 C
HETATM 14 C14 LIG 1 5.731 1.310 0.072 1.00
0.00 C
HETATM 15 C15 LIG 1 6.964 2.215 0.090 1.00
0.00 C
HETATM 16 C16 LIG 1 8.256 1.399 0.032 1.00
0.00 C
HETATM 17 C17 LIG 1 9.487 2.304 0.053 1.00
0.00 C
HETATM 18 C18 LIG 1 10.773 1.497 -0.015 1.00
0.00 C
HETATM 19 H19 LIG 1 -9.046 1.441 -0.329 1.00
0.00 H
HETATM 20 H20 LIG 1 -7.994 2.523 -1.303 1.00
0.00 H
HETATM 21 H21 LIG 1 -8.088 2.727 0.482 1.00
0.00 H
HETATM 22 H22 LIG 1 -6.363 -0.473 1.242 1.00
0.00 H
HETATM 23 H23 LIG 1 -8.119 -0.152 1.164 1.00
0.00 H
HETATM 24 H24 LIG 1 -7.032 1.033 1.966 1.00
0.00 H
HETATM 25 H25 LIG 1 -7.984 -0.423 -1.339 1.00
0.00 H
HETATM 26 H26 LIG 1 -6.237 -0.744 -1.143 1.00
0.00 H
HETATM 27 H27 LIG 1 -6.790 0.563 -2.252 1.00
0.00 H
HETATM 28 H28 LIG 1 -5.710 2.575 0.637 1.00
0.00 H
HETATM 29 H29 LIG 1 -5.632 2.415 -1.133 1.00
0.00 H
HETATM 30 H30 LIG 1 -4.298 0.304 -0.893 1.00
0.00 H
HETATM 31 H31 LIG 1 -4.387 0.429 0.867 1.00
0.00 H
HETATM 32 H32 LIG 1 -3.178 2.601 0.787 1.00
0.00 H
HETATM 33 H33 LIG 1 -3.113 2.511 -0.975 1.00
0.00 H
HETATM 34 H34 LIG 1 -1.796 0.389 -0.824 1.00
0.00 H
HETATM 35 H35 LIG 1 -1.863 0.467 0.938 1.00
0.00 H
HETATM 36 H36 LIG 1 -0.645 2.645 0.903 1.00
0.00 H
HETATM 37 H37 LIG 1 -0.606 2.607 -0.861 1.00
0.00 H
HETATM 38 H38 LIG 1 0.717 0.484 -0.792 1.00
0.00 H
HETATM 39 H39 LIG 1 0.679 0.513 0.972 1.00
0.00 H
HETATM 40 H40 LIG 1 1.891 2.696 0.977 1.00
0.00 H
HETATM 41 H41 LIG 1 1.902 2.705 -0.788 1.00
0.00 H
HETATM 42 H42 LIG 1 3.230 0.584 -0.796 1.00
0.00 H
HETATM 43 H43 LIG 1 3.222 0.568 0.969 1.00
0.00 H
HETATM 44 H44 LIG 1 4.425 2.757 1.007 1.00
0.00 H
HETATM 45 H45 LIG 1 4.412 2.804 -0.758 1.00
0.00 H
HETATM 46 H46 LIG 1 5.745 0.687 -0.830 1.00
0.00 H
HETATM 47 H47 LIG 1 5.760 0.633 0.934 1.00
0.00 H
HETATM 48 H48 LIG 1 6.956 2.828 1.000 1.00
0.00 H
HETATM 49 H49 LIG 1 6.927 2.903 -0.764 1.00
0.00 H
HETATM 50 H50 LIG 1 8.264 0.789 -0.880 1.00
0.00 H
HETATM 51 H51 LIG 1 8.293 0.708 0.883 1.00
0.00 H
HETATM 52 H52 LIG 1 9.489 2.908 0.968 1.00
0.00 H
HETATM 53 H53 LIG 1 9.453 2.999 -0.794 1.00
0.00 H
HETATM 54 H54 LIG 1 10.853 0.812 0.835 1.00
0.00 H
HETATM 55 H55 LIG 1 11.641 2.164 0.003 1.00
0.00 H
HETATM 56 H56 LIG 1 10.818 0.908 -0.937 1.00
0.00 H
CONECT 1 2 3 4 5
CONECT 2 1 19 20 21
CONECT 3 1 22 23 24
CONECT 4 1 25 26 27
CONECT 5 1 6 28 29
CONECT 6 5 7 30 31
CONECT 7 6 8 32 33
CONECT 8 7 9 34 35
CONECT 9 8 10 36 37
CONECT 10 9 11 38 39
CONECT 11 10 12 40 41
CONECT 12 11 13 42 43
CONECT 13 12 14 44 45
CONECT 14 13 15 46 47
CONECT 15 14 16 48 49
CONECT 16 15 17 50 51
CONECT 17 16 18 52 53
CONECT 18 17 54 55 56
CONECT 19 2
CONECT 20 2
CONECT 21 2
CONECT 22 3
CONECT 23 3
CONECT 24 3
CONECT 25 4
CONECT 26 4
CONECT 27 4
CONECT 28 5
CONECT 29 5
CONECT 30 6
CONECT 31 6
CONECT 32 7
CONECT 33 7
CONECT 34 8
CONECT 35 8
CONECT 36 9
CONECT 37 9
CONECT 38 10
CONECT 39 10
CONECT 40 11
CONECT 41 11
CONECT 42 12
CONECT 43 12
CONECT 44 13
CONECT 45 13
CONECT 46 14
CONECT 47 14
CONECT 48 15
CONECT 49 15
CONECT 50 16
CONECT 51 16
CONECT 52 17
CONECT 53 17
CONECT 54 18
CONECT 55 18
CONECT 56 18
MASTER 0 0 0 0 0 0 0 0 56 0 56 0
END
;
; OPLS-AA topology, built by TopolGen version 1.1_dev (10/14/2009)
; Script written by: Justin Lemkul ([email protected])
; This is your molecule's topology
; Check it carefully for any errors. It is not necessarily perfect!
;
; Topology written on lun jun 14 23:45:26 CLT 2010
;
; Include force field
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_287 1 LIG N1 1 -0.300
14.00670
2 opls_516 1 LIG C2 2 0.000
12.01100
3 opls_516 1 LIG C3 3 0.000
12.01100
4 opls_516 1 LIG C4 4 0.000
12.01100
5 opls_516 1 LIG C5 5 0.000
12.01100
6 opls_516 1 LIG C6 6 0.000
12.01100
7 opls_516 1 LIG C7 7 0.000
12.01100
8 opls_516 1 LIG C8 8 0.000
12.01100
9 opls_516 1 LIG C9 9 0.000
12.01100
10 opls_516 1 LIG C10 10 0.000
12.01100
11 opls_516 1 LIG C11 11 0.000
12.01100
12 opls_516 1 LIG C12 12 0.000
12.01100
13 opls_516 1 LIG C13 13 0.000
12.01100
14 opls_516 1 LIG C14 14 0.000
12.01100
15 opls_516 1 LIG C15 15 0.000
12.01100
16 opls_135 1 LIG C16 16 -0.180
12.01100
17 opls_135 1 LIG C17 17 -0.180
12.01100
18 opls_135 1 LIG C18 18 -0.180
12.01100
19 opls_140 1 LIG H19 18 0.060
1.00800
20 opls_140 1 LIG H20 18 0.060
1.00800
21 opls_140 1 LIG H21 18 0.060
1.00800
22 opls_140 1 LIG H22 18 0.060
1.00800
23 opls_140 1 LIG H23 18 0.060
1.00800
24 opls_140 1 LIG H24 18 0.060
1.00800
25 opls_140 1 LIG H25 18 0.060
1.00800
26 opls_140 1 LIG H26 18 0.060
1.00800
27 opls_140 1 LIG H27 18 0.060
1.00800
28 opls_140 1 LIG H28 18 0.060
1.00800
29 opls_140 1 LIG H29 18 0.060
1.00800
30 opls_140 1 LIG H30 18 0.060
1.00800
31 opls_140 1 LIG H31 18 0.060
1.00800
32 opls_140 1 LIG H32 18 0.060
1.00800
33 opls_140 1 LIG H33 18 0.060
1.00800
34 opls_140 1 LIG H34 18 0.060
1.00800
35 opls_140 1 LIG H35 18 0.060
1.00800
36 opls_140 1 LIG H36 18 0.060
1.00800
37 opls_140 1 LIG H37 18 0.060
1.00800
38 opls_140 1 LIG H38 18 0.060
1.00800
39 opls_140 1 LIG H39 18 0.060
1.00800
40 opls_140 1 LIG H40 18 0.060
1.00800
41 opls_140 1 LIG H41 18 0.060
1.00800
42 opls_140 1 LIG H42 18 0.060
1.00800
43 opls_140 1 LIG H43 18 0.060
1.00800
44 opls_140 1 LIG H44 18 0.060
1.00800
45 opls_140 1 LIG H45 18 0.060
1.00800
46 opls_140 1 LIG H46 18 0.060
1.00800
47 opls_140 1 LIG H47 18 0.060
1.00800
48 opls_140 1 LIG H48 18 0.060
1.00800
49 opls_140 1 LIG H49 18 0.060
1.00800
50 opls_140 1 LIG H50 18 0.060
1.00800
51 opls_140 1 LIG H51 18 0.060
1.00800
52 opls_140 1 LIG H52 18 0.060
1.00800
53 opls_140 1 LIG H53 18 0.060
1.00800
54 opls_140 1 LIG H54 18 0.060
1.00800
55 opls_140 1 LIG H55 18 0.060
1.00800
56 opls_140 1 LIG H56 18 0.060
1.00800
[ bonds ]
; ai aj funct
1 2 1 ; N1 C2
1 3 1 ; N1 C3
1 4 1 ; N1 C4
1 5 1 ; N1 C5
2 19 1 ; C2 H19
2 20 1 ; C2 H20
2 21 1 ; C2 H21
3 22 1 ; C3 H22
3 23 1 ; C3 H23
3 24 1 ; C3 H24
4 25 1 ; C4 H25
4 26 1 ; C4 H26
4 27 1 ; C4 H27
5 6 1 ; C5 C6
5 28 1 ; C5 H28
5 29 1 ; C5 H29
6 7 1 ; C6 C7
6 30 1 ; C6 H30
6 31 1 ; C6 H31
7 8 1 ; C7 C8
7 32 1 ; C7 H32
7 33 1 ; C7 H33
8 9 1 ; C8 C9
8 34 1 ; C8 H34
8 35 1 ; C8 H35
9 10 1 ; C9 C10
9 36 1 ; C9 H36
9 37 1 ; C9 H37
10 11 1 ; C10 C11
10 38 1 ; C10 H38
10 39 1 ; C10 H39
11 12 1 ; C11 C12
11 40 1 ; C11 H40
11 41 1 ; C11 H41
12 13 1 ; C12 C13
12 42 1 ; C12 H42
12 43 1 ; C12 H43
13 14 1 ; C13 C14
13 44 1 ; C13 H44
13 45 1 ; C13 H45
14 15 1 ; C14 C15
14 46 1 ; C14 H46
14 47 1 ; C14 H47
15 16 1 ; C15 C16
15 48 1 ; C15 H48
15 49 1 ; C15 H49
16 17 1 ; C16 C17
16 50 1 ; C16 H50
16 51 1 ; C16 H51
17 18 1 ; C17 C18
17 52 1 ; C17 H52
17 53 1 ; C17 H53
18 54 1 ; C18 H54
18 55 1 ; C18 H55
18 56 1 ; C18 H56
[ pairs ]
; ai aj funct
2 22 1 ; C2 H22
2 23 1 ; C2 H23
2 24 1 ; C2 H24
2 25 1 ; C2 H25
2 26 1 ; C2 H26
2 27 1 ; C2 H27
2 6 1 ; C2 C6
2 28 1 ; C2 H28
2 29 1 ; C2 H29
3 25 1 ; C3 H25
3 26 1 ; C3 H26
3 27 1 ; C3 H27
3 6 1 ; C3 C6
3 28 1 ; C3 H28
3 29 1 ; C3 H29
4 6 1 ; C4 C6
4 28 1 ; C4 H28
4 29 1 ; C4 H29
1 7 1 ; C5 C7
1 30 1 ; C5 H30
1 31 1 ; C5 H31
5 8 1 ; C6 C8
5 32 1 ; C6 H32
5 33 1 ; C6 H33
6 9 1 ; C7 C9
6 34 1 ; C7 H34
6 35 1 ; C7 H35
7 10 1 ; C8 C10
7 36 1 ; C8 H36
7 37 1 ; C8 H37
8 11 1 ; C9 C11
8 38 1 ; C9 H38
8 39 1 ; C9 H39
9 12 1 ; C10 C12
9 40 1 ; C10 H40
9 41 1 ; C10 H41
10 13 1 ; C11 C13
10 42 1 ; C11 H42
10 43 1 ; C11 H43
11 14 1 ; C12 C14
11 44 1 ; C12 H44
11 45 1 ; C12 H45
12 15 1 ; C13 C15
12 46 1 ; C13 H46
12 47 1 ; C13 H47
13 16 1 ; C14 C16
13 48 1 ; C14 H48
13 49 1 ; C14 H49
14 17 1 ; C15 C17
14 50 1 ; C15 H50
14 51 1 ; C15 H51
15 18 1 ; C16 C18
15 52 1 ; C16 H52
15 53 1 ; C16 H53
16 54 1 ; C17 H54
16 55 1 ; C17 H55
16 56 1 ; C17 H56
[ angles ]
; ai aj ak funct
2 1 3 1 ; C2 N1 C3
2 1 4 1 ; C2 N1 C4
2 1 5 1 ; C2 N1 C5
1 2 19 1 ; C2 N1 H19
1 2 20 1 ; C2 N1 H20
1 2 21 1 ; C2 N1 H21
3 1 4 1 ; C3 N1 C4
3 1 5 1 ; C3 N1 C5
1 3 22 1 ; C3 N1 H22
1 3 23 1 ; C3 N1 H23
1 3 24 1 ; C3 N1 H24
4 1 5 1 ; C4 N1 C5
1 4 25 1 ; C4 N1 H25
1 4 26 1 ; C4 N1 H26
1 4 27 1 ; C4 N1 H27
1 5 6 1 ; C5 N1 C6
1 5 28 1 ; C5 N1 H28
1 5 29 1 ; C5 N1 H29
19 2 20 1 ; H19 C2 H20
19 2 21 1 ; H19 C2 H21
20 2 21 1 ; H20 C2 H21
22 3 23 1 ; H22 C3 H23
22 3 24 1 ; H22 C3 H24
23 3 24 1 ; H23 C3 H24
25 4 26 1 ; H25 C4 H26
25 4 27 1 ; H25 C4 H27
26 4 27 1 ; H26 C4 H27
6 5 28 1 ; C6 C5 H28
6 5 29 1 ; C6 C5 H29
5 6 7 1 ; C6 C5 C7
5 6 30 1 ; C6 C5 H30
5 6 31 1 ; C6 C5 H31
28 5 29 1 ; H28 C5 H29
7 6 30 1 ; C7 C6 H30
7 6 31 1 ; C7 C6 H31
6 7 8 1 ; C7 C6 C8
6 7 32 1 ; C7 C6 H32
6 7 33 1 ; C7 C6 H33
30 6 31 1 ; H30 C6 H31
8 7 32 1 ; C8 C7 H32
8 7 33 1 ; C8 C7 H33
7 8 9 1 ; C8 C7 C9
7 8 34 1 ; C8 C7 H34
7 8 35 1 ; C8 C7 H35
32 7 33 1 ; H32 C7 H33
9 8 34 1 ; C9 C8 H34
9 8 35 1 ; C9 C8 H35
8 9 10 1 ; C9 C8 C10
8 9 36 1 ; C9 C8 H36
8 9 37 1 ; C9 C8 H37
34 8 35 1 ; H34 C8 H35
10 9 36 1 ; C10 C9 H36
10 9 37 1 ; C10 C9 H37
9 10 11 1 ; C10 C9 C11
9 10 38 1 ; C10 C9 H38
9 10 39 1 ; C10 C9 H39
36 9 37 1 ; H36 C9 H37
11 10 38 1 ; C11 C10 H38
11 10 39 1 ; C11 C10 H39
10 11 12 1 ; C11 C10 C12
10 11 40 1 ; C11 C10 H40
10 11 41 1 ; C11 C10 H41
38 10 39 1 ; H38 C10 H39
12 11 40 1 ; C12 C11 H40
12 11 41 1 ; C12 C11 H41
11 12 13 1 ; C12 C11 C13
11 12 42 1 ; C12 C11 H42
11 12 43 1 ; C12 C11 H43
40 11 41 1 ; H40 C11 H41
13 12 42 1 ; C13 C12 H42
13 12 43 1 ; C13 C12 H43
12 13 14 1 ; C13 C12 C14
12 13 44 1 ; C13 C12 H44
12 13 45 1 ; C13 C12 H45
42 12 43 1 ; H42 C12 H43
14 13 44 1 ; C14 C13 H44
14 13 45 1 ; C14 C13 H45
13 14 15 1 ; C14 C13 C15
13 14 46 1 ; C14 C13 H46
13 14 47 1 ; C14 C13 H47
44 13 45 1 ; H44 C13 H45
15 14 46 1 ; C15 C14 H46
15 14 47 1 ; C15 C14 H47
14 15 16 1 ; C15 C14 C16
14 15 48 1 ; C15 C14 H48
14 15 49 1 ; C15 C14 H49
46 14 47 1 ; H46 C14 H47
16 15 48 1 ; C16 C15 H48
16 15 49 1 ; C16 C15 H49
15 16 17 1 ; C16 C15 C17
15 16 50 1 ; C16 C15 H50
15 16 51 1 ; C16 C15 H51
48 15 49 1 ; H48 C15 H49
17 16 50 1 ; C17 C16 H50
17 16 51 1 ; C17 C16 H51
16 17 18 1 ; C17 C16 C18
16 17 52 1 ; C17 C16 H52
16 17 53 1 ; C17 C16 H53
50 16 51 1 ; H50 C16 H51
18 17 52 1 ; C18 C17 H52
18 17 53 1 ; C18 C17 H53
17 18 54 1 ; C18 C17 H54
17 18 55 1 ; C18 C17 H55
17 18 56 1 ; C18 C17 H56
52 17 53 1 ; H52 C17 H53
54 18 55 1 ; H54 C18 H55
54 18 56 1 ; H54 C18 H56
55 18 56 1 ; H55 C18 H56
[ dihedrals ]
; ai aj ak al funct
2 1 3 22 3 ; C2 N1 C3 H22
2 1 3 23 3 ; C2 N1 C3 H23
2 1 3 24 3 ; C2 N1 C3 H24
2 1 4 25 3 ; C2 N1 C4 H25
2 1 4 26 3 ; C2 N1 C4 H26
2 1 4 27 3 ; C2 N1 C4 H27
2 1 5 6 3 ; C2 N1 C5 C6
2 1 5 28 3 ; C2 N1 C5 H28
2 1 5 29 3 ; C2 N1 C5 H29
3 1 4 25 3 ; C3 N1 C4 H25
3 1 4 26 3 ; C3 N1 C4 H26
3 1 4 27 3 ; C3 N1 C4 H27
3 1 5 6 3 ; C3 N1 C5 C6
3 1 5 28 3 ; C3 N1 C5 H28
3 1 5 29 3 ; C3 N1 C5 H29
4 1 5 6 3 ; C4 N1 C5 C6
4 1 5 28 3 ; C4 N1 C5 H28
4 1 5 29 3 ; C4 N1 C5 H29
1 5 6 7 3 ; C5 N1 C6 C7
1 5 6 30 3 ; C5 N1 C6 H30
1 5 6 31 3 ; C5 N1 C6 H31
5 6 7 8 3 ; C6 C5 C7 C8
5 6 7 32 3 ; C6 C5 C7 H32
5 6 7 33 3 ; C6 C5 C7 H33
6 7 8 9 3 ; C7 C6 C8 C9
6 7 8 34 3 ; C7 C6 C8 H34
6 7 8 35 3 ; C7 C6 C8 H35
7 8 9 10 3 ; C8 C7 C9 C10
7 8 9 36 3 ; C8 C7 C9 H36
7 8 9 37 3 ; C8 C7 C9 H37
8 9 10 11 3 ; C9 C8 C10 C11
8 9 10 38 3 ; C9 C8 C10 H38
8 9 10 39 3 ; C9 C8 C10 H39
9 10 11 12 3 ; C10 C9 C11 C12
9 10 11 40 3 ; C10 C9 C11 H40
9 10 11 41 3 ; C10 C9 C11 H41
10 11 12 13 3 ; C11 C10 C12 C13
10 11 12 42 3 ; C11 C10 C12 H42
10 11 12 43 3 ; C11 C10 C12 H43
11 12 13 14 3 ; C12 C11 C13 C14
11 12 13 44 3 ; C12 C11 C13 H44
11 12 13 45 3 ; C12 C11 C13 H45
12 13 14 15 3 ; C13 C12 C14 C15
12 13 14 46 3 ; C13 C12 C14 H46
12 13 14 47 3 ; C13 C12 C14 H47
13 14 15 16 3 ; C14 C13 C15 C16
13 14 15 48 3 ; C14 C13 C15 H48
13 14 15 49 3 ; C14 C13 C15 H49
14 15 16 17 3 ; C15 C14 C16 C17
14 15 16 50 3 ; C15 C14 C16 H50
14 15 16 51 3 ; C15 C14 C16 H51
15 16 17 18 3 ; C16 C15 C17 C18
15 16 17 52 3 ; C16 C15 C17 H52
15 16 17 53 3 ; C16 C15 C17 H53
16 17 18 54 3 ; C17 C16 C18 H54
16 17 18 55 3 ; C17 C16 C18 H55
16 17 18 56 3 ; C17 C16 C18 H56
[ system ]
; Name
LIG topology, generated by TopolGen
[ molecules ]
; Compound #mols
LIG 1
I also made a methane itp file (below), and the number of angles are
six and not just the five angles with which full angular movement can
be described without redundant coordinates.
; OPLS-AA topology, built by TopolGen version 1.1_dev (10/14/2009)
; Script written by: Justin Lemkul ([email protected])
; This is your molecule's topology
; Check it carefully for any errors. It is not necessarily perfect!
;
; Topology written on mié jun 16 12:52:14 CLT 2010
;
; Include force field
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_135 1 LIG C 1 -0.180 12.01100
2 opls_140 1 LIG H 1 0.060 1.00800
3 opls_140 1 LIG H 1 0.060 1.00800
4 opls_140 1 LIG H 1 0.060 1.00800
5 opls_140 1 LIG H 1 0.060 1.00800
[ bonds ]
; ai aj funct
1 2 1 ; C H
1 3 1 ; C H
1 4 1 ; C H
1 5 1 ; C H
[ pairs ]
; ai aj funct
[ angles ]
; ai aj ak funct
2 1 3 1 ; H C H
2 1 4 1 ; H C H
2 1 5 1 ; H C H
3 1 4 1 ; H C H
3 1 5 1 ; H C H
4 1 5 1 ; H C H
[ dihedrals ]
; ai aj ak al funct
[ system ]
; Name
LIG topology, generated by TopolGen
[ molecules ]
; Compound #mols
LIG 1
> Date: Wed, 16 Jun 2010 07:00:16 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] redundancies in the .itp file
>
>
>
> Víctor Bahamonde wrote:
> > Dear users
> >
> >
> > I have created a .itp file with the program TopolGen, published in the
> > website of GROMACS. to review the angles, I see that there are
> > redundancies. This will affect the results of molecular dynamics
> > calculation?. What should I do with them? (delete?)
> > Thanks in advance!
> >
>
> I've never seen this happen before. Could you send me your coordinate
file and
> resulting topology (off-list) so I can debug?
>
> -Justin
>
> >
> >
------------------------------------------------------------------------
> > Ahora Hotmail es un 70% más veloz. Acceder a tu casilla nunca fue tan
> > rápido. Ver más <http://www.descubrehotmail.com/velocidad.asp >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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------------------------------------------------------------------------
Acceder a tu casilla ahora es mucho más rápido. Ahora Hotmail es un 70%
más veloz. Conoce más <http://www.descubrehotmail.com/velocidad.asp >
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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