[gmx-users] Dihedral not counted?
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 27 17:01:12 CET 2008
Well, there's no real problem, per se. Everything that you've given pdb2gmx is
in the topology; the issue is that you haven't specified any parameters for
those dihedrals:
CH CB CG1 CG2
CH CB CG5 CG4
2 3 4 5 1
2 3 8 7 1
Makes sense that they'd be missing. If you're dealing with polystyrene, maybe
consider basing the dihedrals off of those contained in the PHE sidechain in the
Gromos force field you appear to be using.
-Justin
Andrea Muntean wrote:
> Here are the .rtp entries:
>
>
> [PS1]
> [atoms]
> CH3 CH3 0 0
> CH CH1 0 0
> CB C 0 0
> CG1 CR1 0 0
> CG2 CR1 0 0
> CG3 CR1 0 0
> CG4 CR1 0 0
> CG5 CR1 0 0
>
> [bonds]
> CH3 CH gb_26
> CH CB gb_26
> CB CG1 gb_15
> CG1 CG2 gb_15
> CG2 CG3 gb_15
> CG3 CG4 gb_15
> CG4 CG5 gb_15
> CG5 CB gb_15
> CH +CH2 gb_26
>
> [angles]
> ;109,5 angle
> CH3 CH +CH2 ga_12
> CH3 CH CB ga_12
> CB CH +CH2 ga_12
> ;120 angle
> CH CB CG1 ga_26
> CH CB CG5 ga_26
> CG1 CB CG5 ga_26
> CB CG1 CG2 ga_26
> CG1 CG2 CG3 ga_26
> CG2 CG3 CG4 ga_26
> CG3 CG4 CG5 ga_26
> CG4 CG5 CB ga_26
>
> [impropers]
> ;keep the planarity of the ring
> CB CG1 CG2 CG3 gi_1
> CG1 CG2 CG3 CG4 gi_1
> CG2 CG3 CG4 CG5 gi_1
> CG3 CG4 CG5 CB gi_1
> CG4 CG5 CB CG1 gi_1
> CG5 CB CG1 CG2 gi_1
> ;around CB
> CB CG1 CG5 CH gi_1
> CB CG5 CH CG1 gi_1
> CB CH CG1 CG5 gi_1
> ;around CH
> CH CB +CH2 CH3 gi_1
> CH +CH2 CH3 CB gi_1
> CH CH3 CB +CH2 gi_1
>
> [dihedrals]
> ;in the chain - 3-fold (n=3)
> CH3 CH +CH2 +CH gd_16
> CB CH +CH2 +CH gd_16
> ;around CH-CB - 2-fold (n=2)
> CH3 CH CB CG5 gd_1
> CH3 CH CB CG1 gd_1
> +CH2 CH CB CG5 gd_1
> +CH2 CH CB CG1 gd_1
> ;around CB-CG - 2-fold?,do we need them?
> CH CB CG1 CG2
> CH CB CG5 CG4
>
>
> [PS]
> [atoms]
> CH2 CH2 0 0
> CH CH1 0 0
> CB C 0 0
> CG1 CR1 0 0
> CG2 CR1 0 0
> CG3 CR1 0 0
> CG4 CR1 0 0
> CG5 CR1 0 0
>
> [bonds]
> -CH CH2 gb_26
> CH2 CH gb_26
> CH CB gb_26
> CB CG1 gb_15
> CG1 CG2 gb_15
> CG2 CG3 gb_15
> CG3 CG4 gb_15
> CG4 CG5 gb_15
> CG5 CB gb_15
> CH +CH2 gb_26
>
> [angles]
> ;109,5 angle
> -CH CH2 CH ga_12
> CH2 CH +CH2 ga_12
> CH2 CH CB ga_12
> CB CH +CH2 ga_12
> ;120 angle
> CH CB CG1 ga_26
> CH CB CG5 ga_26
> CG1 CB CG5 ga_26
> CB CG1 CG2 ga_26
> CG1 CG2 CG3 ga_26
> CG2 CG3 CG4 ga_26
> CG3 CG4 CG5 ga_26
> CG4 CG5 CB ga_26
>
> [impropers]
> ;keep the planarity of the ring
> CB CG1 CG2 CG3 gi_1
> CG1 CG2 CG3 CG4 gi_1
> CG2 CG3 CG4 CG5 gi_1
> CG3 CG4 CG5 CB gi_1
> CG4 CG5 CB CG1 gi_1
> CG5 CB CG1 CG2 gi_1
> ;around CB
> CB CG1 CG5 CH gi_1
> CB CG5 CH CG1 gi_1
> CB CH CG1 CG5 gi_1
> ;around CH
> CH CB +CH2 CH2 gi_1
> CH +CH2 CH2 CB gi_1
> CH CH2 CB +CH2 gi_1
>
> [dihedrals]
> ;in the chain - 3-fold
> CH2 CH +CH2 +CH gd_16
> CB CH +CH2 +CH gd_16
> -CH CH2 CH CB gd_16
> -CH CH2 CH +CH2 gd_16
> ;around CH-CB - 2-fold
> CH2 CH CB CG5 gd_1
> CH2 CH CB CG1 gd_1
> +CH2 CH CB CG5 gd_1
> +CH2 CH CB CG1 gd_1
> ;around CB-CG - 2-fold?,do we need them?
> CH CB CG1 CG2
> CH CB CG5 CG4
>
> [ PSN ]
> [atoms]
> CH2 CH2 0 0
> CH CH1 0 0
> CB C 0 0
> CG1 CR1 0 0
> CG2 CR1 0 0
> CG3 CR1 0 0
> CG4 CR1 0 0
> CG5 CR1 0 0
> CH3 CH3 0 0
>
> [bonds]
> -CH CH2 gb_26
> CH2 CH gb_26
> CH CB gb_26
> CB CG1 gb_15
> CG1 CG2 gb_15
> CG2 CG3 gb_15
> CG3 CG4 gb_15
> CG4 CG5 gb_15
> CG5 CB gb_15
> CH CH3 gb_26
>
> [angles]
> -CH CH2 CH ga_12
> CH2 CH CH3 ga_12
> CH2 CH CB ga_12
> CB CH CH3 ga_12
> CH CB CG1 ga_26
> CH CB CG5 ga_26
> CG1 CB CG5 ga_26
> CB CG1 CG2 ga_26
> CG1 CG2 CG3 ga_26
> CG2 CG3 CG4 ga_26
> CG3 CG4 CG5 ga_26
> CG4 CG5 CB ga_26
>
> [impropers]
> ;keep the planarity of the ring
> CB CG1 CG2 CG3 gi_1
> CG1 CG2 CG3 CG4 gi_1
> CG2 CG3 CG4 CG5 gi_1
> CG3 CG4 CG5 CB gi_1
> CG4 CG5 CB CG1 gi_1
> CG5 CB CG1 CG2 gi_1
> ;around CB
> CB CG1 CG5 CH gi_1
> CB CG5 CH CG1 gi_1
> CB CH CG1 CG5 gi_1
> ;around CH
> CH CB CH3 CH2 gi_1
> CH CH3 CH2 CB gi_1
> CH CH2 CB CH3 gi_1
>
> [dihedrals]
> ;in the chain - 3-fold (n=3)
> -CH CH2 CH CB gd_16
> -CH CH2 CH CH3 gd_16
> ;around CH-CB - 2-fold (n=2)
> CH2 CH CB CG5 gd_1
> CH2 CH CB CG1 gd_1
> CH3 CH CB CG5 gd_1
> CH3 CH CB CG1 gd_1
> ;around CB-CG - 2-fold?,do we need them?
> CH CB CG1 CG2
> CH CB CG5 CG4
> CB CG1 CG5 CH gi_1
> CB CG5 CH CG1 gi_1
> CB CH CG1 CG5 gi_1
> ;around CH
> CH CB CH3 CH2 gi_1
> CH CH3 CH2 CB gi_1
> CH CH2 CB CH3 gi_1
>
> [dihedrals]
> ;in the chain - 3-fold (n=3)
> -CH CH2 CH CB gd_16
> -CH CH2 CH CH3 gd_16
> ;around CH-CB - 2-fold (n=2)
> CH2 CH CB CG5 gd_1
> CH2 CH CB CG1 gd_1
> CH3 CH CB CG5 gd_1
> CH3 CH CB CG1 gd_1
> ;around CB-CG - 2-fold?,do we need them?
> CH CB CG1 CG2
> CH CB CG5 CG4
>
>
> And the .top file for the trimer, only the [atoms] and [dihedrals]
> (only the proper dihedrals) part:
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 CH3 1 PS1 CH3 1 0 15.035 ; qtot 0
> 2 CH1 1 PS1 CH 1 0 13.019 ; qtot 0
> 3 C 1 PS1 CB 1 0 12.011 ; qtot 0
> 4 CR1 1 PS1 CG1 1 0 13.019 ; qtot 0
> 5 CR1 1 PS1 CG2 1 0 13.019 ; qtot 0
> 6 CR1 1 PS1 CG3 1 0 13.019 ; qtot 0
> 7 CR1 1 PS1 CG4 1 0 13.019 ; qtot 0
> 8 CR1 1 PS1 CG5 1 0 13.019 ; qtot 0
> 9 CH2 2 PS CH2 2 0 14.027 ; qtot 0
> 10 CH1 2 PS CH 2 0 13.019 ; qtot 0
> 11 C 2 PS CB 2 0 12.011 ; qtot 0
> 12 CR1 2 PS CG1 2 0 13.019 ; qtot 0
> 13 CR1 2 PS CG2 2 0 13.019 ; qtot 0
> 14 CR1 2 PS CG3 2 0 13.019 ; qtot 0
> 15 CR1 2 PS CG4 2 0 13.019 ; qtot 0
> 16 CR1 2 PS CG5 2 0 13.019 ; qtot 0
> 17 CH2 3 PSN CH2 3 0 14.027 ; qtot 0
> 18 CH1 3 PSN CH 3 0 13.019 ; qtot 0
> 19 C 3 PSN CB 3 0 12.011 ; qtot 0
> 20 CR1 3 PSN CG1 3 0 13.019 ; qtot 0
> 21 CR1 3 PSN CG2 3 0 13.019 ; qtot 0
> 22 CR1 3 PSN CG3 3 0 13.019 ; qtot 0
> 23 CR1 3 PSN CG4 3 0 13.019 ; qtot 0
> 24 CR1 3 PSN CG5 3 0 13.019 ; qtot 0
> 25 CH3 3 PSN CH3 3 0 15.035 ; qtot 0
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 1 2 3 4 1 gd_1
> 1 2 3 8 1 gd_1
> 9 2 3 4 1 gd_1
> 9 2 3 8 1 gd_1
> 1 2 9 10 1 gd_16
> 3 2 9 10 1 gd_16
> 2 3 4 5 1
> 2 3 8 7 1
> 2 9 10 11 1 gd_16
> 9 10 11 12 1 gd_1
> 9 10 11 16 1 gd_1
> 17 10 11 12 1 gd_1
> 17 10 11 16 1 gd_1
> 9 10 17 18 1 gd_16
> 11 10 17 18 1 gd_16
> 10 11 12 13 1
> 10 11 16 15 1
> 10 17 18 19 1 gd_16
> 10 17 18 25 1 gd_16
> 17 18 19 20 1 gd_1
> 17 18 19 24 1 gd_1
> 25 18 19 20 1 gd_1
> 25 18 19 24 1 gd_1
> 18 19 20 21 1
> 18 19 24 23 1
>
>
> Cheers,
> Andrea
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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