[gmx-users] redundancies in the .itp file
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 16 22:34:49 CEST 2010
Víctor Bahamonde wrote:
> ok, then six angles for methane is fine, but I think five angles should
> also be fine, because it would be an angle as a function of the others
> already defined. therefore, is there any difference between the two
> previous situations?, is there no redundancy by adding the 6 angles and
> not just 5? I also made the itp file for the carbonate ion, and the
> number of defined angles are 3, but I think (again) one of them is a
> function on the others two, so, is this a redundancy?
>
It depends entirely upon the application. If you're constraining your molecule
to make it rigid, there likely won't be much of a difference, but your structure
could (in theory) deviate somewhat if you are using only harmonic potentials.
By explicitly defining all angles, you remove any doubt about what's going on.
I'd say it's better to be safe than sorry.
One way to prove this to yourself is to run a short MD simulation of this single
molecule and see how the changes affect it.
Do heed the warning in the header of your topology file. The charges on the
carboxylate are certainly wrong, since in theory, the oxygens should be
equivalent due to resonance.
-Justin
> CO3 ion
>
> COMPND UNNAMED
> AUTHOR GENERATED BY OPEN BABEL 2.2.3
> HETATM 1 C LIG 1 -3.406 2.477 -0.006 1.00
> 0.00 C
> HETATM 2 O LIG 1 -2.228 2.893 0.008 1.00
> 0.00 O
> HETATM 3 O LIG 1 -4.001 2.252 1.069 1.00
> 0.00 O
> HETATM 4 O LIG 1 -3.988 2.287 -1.095 1.00
> 0.00 O
> CONECT 1 2 3 4
> CONECT 2 1
> CONECT 3 1
> CONECT 4 1
> MASTER 0 0 0 0 0 0 0 0 4 0 4 0
> END
>
> ;
> ; OPLS-AA topology, built by TopolGen version 1.1_dev (10/14/2009)
> ; Script written by: Justin Lemkul (jalemkul at vt.edu)
> ; This is your molecule's topology
> ; Check it carefully for any errors. It is not necessarily perfect!
> ;
> ; Topology written on mié jun 16 15:33:32 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_271 1 LIG C 1 0.700 12.01100
> 2 opls_272 1 LIG O 1 -0.800 15.99940
> 3 opls_272 1 LIG O 1 -0.800 15.99940
> 4 opls_236 1 LIG O 1 -0.500 15.99940
>
> [ bonds ]
> ; ai aj funct
> 1 2 1 ; C O
> 1 3 1 ; C O
> 1 4 1 ; C O
>
> [ pairs ]
> ; ai aj funct
>
> *[ angles ]
> ; ai aj ak funct
> 2 1 3 1 ; O C O
> 2 1 4 1 ; O C O
> 3 1 4 1 ; O C O*
>
> [ dihedrals ]
> ; ai aj ak al funct
>
> [ dihedrals ]
> ; aj ak ai al funct
> 2 4 1 3 1 improper_O_C_X_Y ; O
> C O O
>
> [ system ]
> ; Name
> LIG topology, generated by TopolGen
>
> [ molecules ]
> ; Compound #mols
> LIG 1
>
>
> > Date: Wed, 16 Jun 2010 13:46:21 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] redundancies in the .itp file
> >
> >
> > 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 (jalemkul at vt.edu)
> > > ; 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 (jalemkul at vt.edu)
> > > ; 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: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > 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
> > > >
> > > > ========================================
> > > > --
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >
> ------------------------------------------------------------------------
> > > 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
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> ------------------------------------------------------------------------
> Hotmail es más seguro. Con el Filtro Anti Spam tu cuenta está mucho más
> protegida. Ver más <http://www.descubrehotmail.com/anti-spam.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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