[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
>
> ========================================
>



More information about the gromacs.org_gmx-users mailing list