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

Bruce D. Ray brucedray at yahoo.com
Fri Feb 5 23:39:36 CET 2010

On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte <antoinedelmotte at hotmail.com>

> 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
> 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
> 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
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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