[gmx-users] OPLS-AA topologies for ATP/ADP.

[Bruce D. Ray]

On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela

<lucioric at ibt.unam.mx> wrote:

> Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
> forcefield?. If not, how can I parameterize this molecules?.
> Best regards.
>    Lucio Montero.
> 
> Lucio Ricardo Montero Valenzuela
> Instituto de Biotecnologia, UNAM
> Departamento de Biologia Molecular de Plantas
> Av. Universidad 2001, Col. Chamilpa
> Cuernavaca 62210
> Mexico

I've not tested this at all, but from my attempts to add OPLS-AA to topolbuild,
I get the following that might be suitable for insertion in the oplsaa rtp:

[ ATP ]
 [ atoms ]
   O9P    opls_441  -0.635     0 ;O2
   O8P    opls_441  -0.635     1 ;O2
   O7P    opls_441  -0.635     2 ;O2
    PG    opls_445   0.072     3 ;P
   O6P    opls_442  -0.286     4 ;OS
   O5P    opls_441  -0.516     5 ;O2
   O4P    opls_441  -0.516     6 ;O2
    PB    opls_440   0.280     7 ;P
   O3P    opls_442  -0.250     8 ;OS
   O2P    opls_441  -0.516     9 ;O2
   O1P    opls_441  -0.516    10 ;O2
    PA    opls_440   0.276    11 ;P
   O5*    opls_442  -0.315    12 ;OS
   C5*    opls_443   0.085    13 ;CT
  H5*1    opls_444   0.059    14 ;HC
  H5*2    opls_444   0.059    15 ;HC
   C4*    opls_174   0.113    16 ;CT
   H4*    opls_176   0.065    17 ;HC
   O4*    opls_186  -0.348    18 ;OS
   C1*    opls_193   0.160    19 ;CO
   H1*    opls_194   0.084    20 ;HC
    N9    opls_354B -0.245    21 ;NA
    C8    opls_353   0.092    22 ;CK
    H8    opls_359   0.100    23 ;H5
    N7    opls_352  -0.233    24 ;NB
    C5    opls_350   0.145    25 ;CB
    C6    opls_351   0.147    26 ;CA
    N6    opls_356  -0.341    27 ;N2
   H61    opls_357   0.144    28 ;H
   H62    opls_358   0.144    29 ;H
    N1    opls_346  -0.219    30 ;NC
    C2    opls_347   0.120    31 ;CQ
    H2    opls_355   0.066    32 ;H5
    N3    opls_348  -0.218    33 ;NC
    C4    opls_349   0.159    34 ;CB
   C2*    opls_174   0.127    35 ;CT
   H2*    opls_176   0.100    36 ;HC
   O2'    opls_171  -0.385    37 ;OH
   H2'    opls_172   0.210    38 ;HO
   C3*    opls_174   0.113    39 ;CT
   H3*    opls_176   0.065    40 ;HC
   O3'    opls_171  -0.386    41 ;OH
   H3'    opls_172   0.210    42 ;HO
 [ bonds ]
    PG   O9P
    PG   O8P
    PG   O7P
   O6P    PG
    PB   O6P
    PB   O5P
    PB   O4P
   O3P    PB
    PA   O3P
    PA   O2P
    PA   O1P
    PA   O5*
   O5*   C5*
   C5*   C4*
   C5*  H5*1
   C5*  H5*2
   C4*   O4*
   C4*   H4*
   C4*   C3*
   O4*   C1*
   C1*    N9
   C1*   H1*
   C1*   C2*
    N9    C8
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    N6
    N6   H61
    N6   H62
    C6    N1
    N1    C2
    C2    H2
    C2    N3
    N3    C4
    C4    N9
   C2*   C3*
   C2*   H2*
   C2*   O2'
   O2'   H2'
   C3*   H3*
   C3*   O3'
   O3'   H3'


Please let me know if this actually works for computations.
Charges were derived from the .mol2 file generated by Sybyl.


Sincerely,


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273