[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

[Antoine Delmotte]

Thank you very much for this, Bruce. It will help me, for sure.

Could you just let me know where you found the parameters or how you 
generated them?

Thanks in advance.

Regards,

Antoine

Le 5/02/2010 22:39, Bruce D. Ray a écrit :
> On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte 
> <antoinedelmotte at hotmail.com>
> wrote:
> > I would like to simulate the CDK9 protein (3BLH in PDB), but there 
> is one residue (TPO,
> > phosphothreonine), which Gromacs does not recognise.
> >
> > I found the PRODRG website as well as force field parameters for TPO 
> for the Gromos96.1
> > force field. However, I would like to use the OPLS-AA force field. I 
> therefore need a topology
> > file for this force field, which cannot be provided by PRODRG (only 
> useful for united atoms
> > force fields).
> >
> > Does anyone have an idea about where I could get the 
> phosphothreonine itp file for OPLS
> > force field?
> >
> > Otherwise, could someone give me clues or the link to a good 
> tutorial about how to create
> > this itp file myself?
> >
> > Molecular dynamics is something completely new for me so, sorry if I 
> ask stupid questions.
> > It also seems I am not the first one to have this problem but I 
> could not find any solution on
> > the archive of the mailing list.
>
> The charges probably need a little more work, but this might be a 
> start towards an
> rtp file for phosphothreonine to add to ffoplsaa.rtp.
>
> [ TPO ]
>  [ atoms ]
>      N    opls_238   -0.500     1
>      H    opls_241    0.300     1
>     CA    opls_224B   0.140     1
>     HA    opls_140    0.060     1
>     CB    opls_158    0.205     2
>     HB    opls_140    0.060     2
>    OG1    opls_447   -0.700     2
>      P    opls_445    1.795     3
>    O1P    opls_446   -1.120     3
>    O2P    opls_446   -1.120     3
>    O3P    opls_446   -1.120     3
>    CG2    opls_135   -0.180     4
>   HG21    opls_140    0.060     4
>   HG22    opls_140    0.060     4
>   HG23    opls_140    0.060     4
>      C    opls_235    0.500     5
>      O    opls_236   -0.500     5
>  [ bonds ]
>      N     H
>      N    CA
>     CA    HA
>     CA    CB
>     CA     C
>     CB    HB
>     CB   OG1
>     CB   CG2
>    OG1     P
>    O1P     P
>    O2P     P
>    O3P     P
>    CG2  HG21
>    CG2  HG22
>    CG2  HG23
>      C     O
>     -C     N
>  [ dihedrals ] ; override some of the typebased dihedrals
>      N    CA    CB   OG1    dih_SER_THR_chi1_N_C_C_O
>      C    CA    CB   OG1    dih_SER_THR_chi1_CO_C_C_O
>     CA    CB   OG1   HG1    dih_SER_THR_chi2_C_C_OH_HO
>  [ impropers ]
>     -C    CA     N     H    improper_Z_N_X_Y
>     CA    +N     C     O    improper_O_C_X_Y
>
>
> I hope that helps.
>
>
> -- 
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN 46202-3273
>
>

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