[gmx-users] Dihedral not counted?
Andrea Muntean
andreamuntean at gmail.com
Mon Oct 27 19:44:08 CET 2008
Strange enough, those dihedrals are there, but the dihedral between
atoms 2 9 10 and 17 is missing (in the main chain), altough defined in
the PS residue (as -CH CH2 CH +CH2). I am still clueless...
Greetings,
Andrea
2008/10/27 Justin A. Lemkul <jalemkul at vt.edu>:
> 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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