[gmx-users] Regarding ffG43a1p force field

Ramachandran G gtrama at gmail.com
Thu Jun 23 09:39:30 CEST 2011


It is neutral.

I tried sending the coordinates but it bounces. So i paste below the
chromophore coordinates alone.
   64CRIH   CB2  948   2.946   2.849   3.832
   64CRIH   HB2  949   2.948   2.845   3.932
   64CRIH   CA2  950   2.827   2.790   3.770
   64CRIH    N2  951   2.795   2.778   3.639
   64CRIH    C1  952   2.683   2.711   3.636
   64CRIH    N3  953   2.629   2.694   3.756
   64CRIH    C2  954   2.723   2.736   3.850
   64CRIH   OC2  955   2.694   2.757   3.968
   64CRIH   CG2  956   3.059   2.911   3.774
   64CRIH    CZ  957   3.282   3.042   3.676
   64CRIH   CD1  958   3.085   2.912   3.634
   64CRIH   HD1  959   3.023   2.867   3.569
   64CRIH   CD2  960   3.152   2.973   3.862
   64CRIH   HD2  961   3.143   2.961   3.961
   64CRIH   CE1  962   3.198   2.975   3.589
   64CRIH   HE1  963   3.220   2.974   3.492
   64CRIH   CE2  964   3.253   3.048   3.811
   64CRIH   HE2  965   3.307   3.108   3.871
   64CRIH    OH  966   3.391   3.101   3.633
   64CRIH    HH  967   3.439   3.143   3.710
   64CRIH    N   968   2.533   2.768   3.461
   64CRIH    H   969   2.581   2.856   3.437
   64CRIH   CA1  970   2.614   2.661   3.514
   64CRIH   CB1  971   2.714   2.610   3.411
   64CRIH   OG1  972   2.778   2.493   3.461
   64CRIH   HG1  973   2.875   2.504   3.442
   64CRIH   CA3  974   2.494   2.655   3.788
   64CRIH     C  975   2.491   2.532   3.876
   64CRIH     O  976   2.414   2.527   3.972




On Thu, Jun 23, 2011 at 12:34 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Is is this for the neutral chromophore or protonated one ??
>
>
> On Thu, Jun 23, 2011 at 4:29 PM, Ramachandran G <gtrama at gmail.com> wrote:
>
>> yes!
>>
>>
>> On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>
>>> these are in continuity I mean for the ffbonded.itp file
>>>
>>> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G <gtrama at gmail.com>wrote:
>>>
>>>> more parameters - ffbonded.itp
>>>> NB    CT       1    0.1444    294553.6
>>>> NB    C        1    0.1404    334720.0
>>>> C      CC      1    0.1407    343088.0
>>>> CC    CB       1    0.1474    468608.0
>>>>  CB     H2     1    0.1076    129960.25
>>>>
>>>> to aminoacids.hdb
>>>> 1       1       HE2     CE2     CZ      CD2
>>>> 1       1       HE1     CE1     CZ      CD1
>>>> 1       1       HD1     CD1     CG2     CE1
>>>> 1       1       HD2     CD2     CG2     CE2
>>>> 1       2       HH      OH      CZ      CE1
>>>> 1       1       HB2     CB2     CA2     CG2
>>>> 1       2       HG1     OG1     CB1     CA1
>>>> 1       1       H       N      CA1     C1
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jun 23, 2011 at 12:18 AM, Ramachandran G <gtrama at gmail.com>wrote:
>>>>
>>>>> For ffbonded.itp, i added the following. (you need to be carefull here
>>>>> since i cooked upto the force constants)
>>>>>  C     CC    CB    CA    9     180.0   4.309   1
>>>>>  NB    CC    C     O     9     180.0   4.309   1 ;
>>>>>  NB    CC    CB    CA    9     180.0   4.309   1
>>>>>  NB    CC    CB    H2    9     180.0   4.309   1
>>>>>  C     CC    CB    H2    9     180.0   4.309   1
>>>>>  NB    CC    C     NB    9     180.0   4.0876  1
>>>>>  CT    NB    C     CC    9     180.0   4.0876  1
>>>>>  CT    NB    C     O     9     180.0   4.0876  1
>>>>>  CB    CC    C     NB    9     180.0   4.0876  1
>>>>>  CB    CC    C     O     9     180.0   4.0876  1
>>>>>  CC    C     NB    CC    9     180.0   4.7656  1
>>>>>  O     C     NB    CC    9     180.0   4.7656  1;
>>>>>  CC    NB    CT    C     9     180.0   4.1400  1;
>>>>>  C     NB    CT    C     9     180.0   4.1400  1 ;
>>>>>  CT    CT    OH    HO    4     180.0   4.1400  1 ;
>>>>>  OH   CT    CT     CC    9       0.0   4.1400  1
>>>>>  OH   CT    CT     N     9     180.0   4.9162  1
>>>>>
>>>>> ; added newly  improper dihedrals
>>>>>  CB    CC    CA   H2   4       180.0    4.1840 2
>>>>>  CC    NB    CB   C    4       180.0    4.1840 2
>>>>>  CC    CT    NB   NB   4       180.0    4.1840 2
>>>>>  CT    N     CC   CT   4       144.64   3.1840 2
>>>>>  NB    O     CC   C    4       180.0    4.1840 2
>>>>>  NB    CC    C    CT   4       180.0    4.1840 2
>>>>>  CA    CB    CA   CA   4       180.0    4.1840 2
>>>>>  CA    HA    CA   CA   4       180.0    4.1840 2
>>>>> ; added to test
>>>>>  N   CT   C    H    4   180.0    4.1840  2
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Jun 23, 2011 at 12:13 AM, Ramachandran G <gtrama at gmail.com>wrote:
>>>>>
>>>>>> For the GFP chromophore  i name residue as CRIH.
>>>>>> 1. aminoacids.rtp
>>>>>>        CB2     CB     0.019103       1
>>>>>>        CA2     CC    -0.026635       2
>>>>>>        N2      NB    -0.436463       3
>>>>>>        C1      CC     0.302706       4
>>>>>>        N3      NB    -0.541478       5
>>>>>>        C2      C      0.563844       6
>>>>>>        OC2     O     -0.394118       7
>>>>>>        CG2     CA    -0.079330       8
>>>>>>        CZ      CA     0.240178       9
>>>>>>        CD1     CA    -0.072596      10
>>>>>>        HD1     HA     0.129374      11
>>>>>>        CD2     CA    -0.070677      12
>>>>>>        HD2     HA     0.091532      13
>>>>>>        CE1     CA    -0.129374      14
>>>>>>        HE1     HA     0.091792      15
>>>>>>        CE2     CA    -0.087778      16
>>>>>>        HE2     HA     0.112301      17
>>>>>>        OH      OH    -0.454413      18
>>>>>>        H       H      0.37107       19
>>>>>>        HH      HO     0.258435      20
>>>>>>        N       N     -0.61682       21
>>>>>>        CA1     CT    -0.116631      22
>>>>>>        CB1     CT    -0.03127       23
>>>>>>        OG1     OH    -0.74662       24
>>>>>>        HG1     HO     0.45887       25
>>>>>>        HB2     H2     0.116716      26
>>>>>>        CA3     CT    -0.250251      27
>>>>>>        C        C     0.35254       28
>>>>>>        O        O    -0.48366       29
>>>>>>  [ bonds ]
>>>>>>        C1      CA1
>>>>>>        N3      CA3
>>>>>>        N3      C1
>>>>>>        N3      C2
>>>>>>        C2      OC2
>>>>>>        C1      N2
>>>>>>        C2      CA2
>>>>>>        N2      CA2
>>>>>>        CA2     CB2
>>>>>>        CB2     CG2
>>>>>>        CG2     CD1
>>>>>>        CG2     CD2
>>>>>>        CD1     CE1
>>>>>>        CD2     CE2
>>>>>>        CE1     CZ
>>>>>>        CE2     CZ
>>>>>>        CZ      OH
>>>>>>        CB1     OG1
>>>>>>        OH      HH
>>>>>>        CB2     HB2
>>>>>>        CD1     HD1
>>>>>>        CD2     HD2
>>>>>>        CE1     HE1
>>>>>>        CE2     HE2
>>>>>>        CA1     N
>>>>>>        CA1     CB1
>>>>>>        CA3     C
>>>>>>         C      O
>>>>>>        OG1     CB1
>>>>>>        OG1     HG1
>>>>>>         N      H
>>>>>>        -C      N
>>>>>>        +N      C
>>>>>>  [ angles ]
>>>>>>         ;  ai    aj    ak   th0     cth     ub0     cub
>>>>>>           N2   C1   N3     114.0      1087.87
>>>>>>           C1    N2   CA2   106.0      1087.87
>>>>>>           C1    N3   C2    107.9      1087.87
>>>>>>           N2    CA2  C2    108.3     1087.87
>>>>>>           N2    CA2  CB2   129.5      376.56
>>>>>>           C2    N3   CA3   123.4      267.776
>>>>>>           N3    C2   OC2   126.0      351.456
>>>>>>           N3    C2   CA2   103.0     1087.87
>>>>>>           OC2   C2   CA2   132.0      317.984
>>>>>>           C2    CA2  CB2   122.0      376.56
>>>>>>           CA2   CB2  CG2   130.0     1087.87
>>>>>>           CB2   CG2  CD1   121.0      383.2544
>>>>>>           CB2   CG2  CD2   121.0      383.2544
>>>>>>           CG2   CD1  CE1   120.0      334.72
>>>>>>           CG2   CD2  CE2   120.0      334.72
>>>>>>           CD1   CG2  CD2   120.0      334.72
>>>>>>           CD1   CE1  CZ    120.0      334.72
>>>>>>           CD2   CE2  CZ    120.0      334.72
>>>>>>           CE1   CZ  CE2    120.0      334.72
>>>>>>           OH    CZ  CE1    120.0      378.2336
>>>>>>           OH    CZ  CE2    120.0      378.2336
>>>>>>           HH    OH   CZ    108.0      543.92
>>>>>>           HG1   OG1  CB1   108.0      543.92
>>>>>>           N2    C1   CA1   125.0      334.72
>>>>>>           N3    C1   CA1   121.4      292.88
>>>>>>           C1    N3  CA3    129.0      301.248
>>>>>>           HB2   CB2  CA2   114.0      351.456
>>>>>>           HB2   CB2  CG2   116.0      351.456
>>>>>>           HD1   CD1  CG2   120.0      251.04
>>>>>>           HD1   CD1  CE1   120.0      251.04
>>>>>>           HD2   CD2  CG2   120.0      251.04
>>>>>>           HD2   CD2  CE2   120.0      251.04
>>>>>>           HE1   CE1  CZ    120.0      251.04
>>>>>>           HE1   CE1  CD1   120.0      251.04
>>>>>>           HE2   CE2  CZ    120.0      251.04
>>>>>>           HE2   CE2  CD2   120.0      251.04
>>>>>>            CA1   N    H     118.4      317.984
>>>>>>            CA1   CB1  OG1   109.5      669.44
>>>>>>            N     CA1  CB1   109.7      669.44
>>>>>>            CB1   CA1  C1    111.1      527.184
>>>>>>           CA3   C    O     120.4      669.44
>>>>>>            N     CA1  C1    110.1      527.184
>>>>>>           C     CA3  N3    110.3      669.44
>>>>>>           CA3   C    N     116.6      585.76
>>>>>>           C2    CA2   CB2    CG2 ;
>>>>>>           N2    CA2   CB2    CG2
>>>>>>           CA2   CB2   CG2   CD1 ;
>>>>>>           CA2   CB2   CG2   CD2 ;
>>>>>>           N2    CA2   CB2   HB2
>>>>>>           C2    CA2   CB2   HB2
>>>>>>           HB2   CB2   CG2   CD1 ;
>>>>>>           HB2   CB2   CG2   CD2 ;
>>>>>>           CB2   CG2   CD1   CE1 ;
>>>>>>           CB2   CG2   CD2   CE2 ;
>>>>>>           CD1   CE1   CZ    CE2
>>>>>>           CD1   CE1   CZ    OH
>>>>>>           CE1   CZ    OH    HH
>>>>>>           CE2   CZ    OH    HH
>>>>>>           CG2   CD1   CE1   CZ
>>>>>>           HD1   CD1   CG2   CD2
>>>>>>           HD1   CD1   CE1   CZ
>>>>>>           HD2   CD2   CG2   CD1
>>>>>>           HD2   CD2   CE2   CZ
>>>>>>           HE1   CE1   CD1   CG2
>>>>>>           HE1   CE1   CZ    CE2
>>>>>>           HE2   CE2   CD2   CG2
>>>>>>           HE2   CE2   CZ    CE1
>>>>>>           CA1   C1     N2   CA2 ;
>>>>>>           CA1   C1     N3   C2  ;
>>>>>>           CA3   N3     C2   CA2
>>>>>>           CA3   N3     C1   N2  ;
>>>>>>           CG2   CB2    CA2  N2  ; repeated
>>>>>>           CG2   CB2    CA2  C2  ; repeated
>>>>>>           CB2   CA2    N2   C1
>>>>>>           CB2   CA2    C2   N3
>>>>>>           CA2   N2     C1   N3
>>>>>>           CA2   C2     N3   C1
>>>>>>           OG1   CB1    CA1  C1  ;
>>>>>>           OG1   CB1    CA1  N   ;
>>>>>>           CA1   CB1    OG1  HG1  ;
>>>>>>           N3    CA3    C    O   ;
>>>>>>           OC2   C2    CA2  CB2  ;
>>>>>>           OC2   C2    N3   CA3  ;
>>>>>>           OC2   C2    CA2  N2   ;
>>>>>>           OC2   C2    N3   C1   ;
>>>>>>           N3    CA3    C   +N  ;  added to link the neighbouring
>>>>>> valine
>>>>>>           CA3    C    +N   +H  ;
>>>>>>           CA3    C    +N   +CA  ;
>>>>>>           CB1   CA1    N   -C   ;  added to link the neighbouring PHE
>>>>>>           C1    CA1    N   -C   ;
>>>>>>           CA1    N    -C   -O   ;
>>>>>>            H     N    -C   -O   ; n
>>>>>>  [ impropers ]
>>>>>>            C1     CA1   N2     N3
>>>>>>            CA2    N2    CB2    C2
>>>>>>            C2     CA2   OC2    N3
>>>>>>            CG2    CB2   CD1    CD2
>>>>>>            CZ     CE1   CE2    OH
>>>>>>            N3     C1    C2     CA3
>>>>>>            CB2    CA2   CG2    HB2
>>>>>>            CD1    CG2   HD1    CE1
>>>>>>            CD2    CG2   HD2    CE2
>>>>>>            CE1    CD1   HE1    CZ
>>>>>>            CE2    CD2   HE2    CZ
>>>>>>            CA1    N     C1     CB1
>>>>>>            C      CA3    N     O  ;
>>>>>>            N      CA1    C     H  ;
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Postdoctoral Research Scholar,
>>>>> Department of Chemistry,
>>>>> University of Nevada, Reno.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Postdoctoral Research Scholar,
>>>> Department of Chemistry,
>>>> University of Nevada, Reno.
>>>>
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46010 at yahoo.com
>>>
>>>
>>> --
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>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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