[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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