[gmx-users] Phosphohistidine parameters

Thu Feb 7 12:30:33 CET 2008

Hi,
I have been working quite extyensively with phosphoHIS(HIP), and would
be glad to share rtp entry I developed for my own work.

Although I came across this paper
Kosinsky et. al. Development of the forcefield parameters for
phosphoimidazole and phosphohistidine. Journal of Comp. Chem. Vol 25 No. 11

But, finally I developed my own. Here is the rtp entry.
Your work will also help validate.

[ HIP ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG     C     0.06000     2
  ND1    NR    -0.50000     2
  HD1     H     0.30000     2
  CD2   CR1     0.25000     2
  CE1   CR1     0.45000     2
  NE2    NR    -0.38000     2
    P     P     1.03000     3
  O1P    OM    -0.78000     3
  O2P    OM    -0.78000     3
  O3P    OA    -0.65000     3
    C     C       0.380     4
    O     O      -0.380     4
[ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    CG    gb_26
   CG   ND1    gb_9
   CG   CD2    gb_9
  ND1   HD1    gb_2
  ND1   CE1    gb_9
  CD2   NE2    gb_9
  CE1   NE2    gb_9
  NE2     P    0.184   2803599.6
    P   O1P    gb_23
    P   O2P    gb_23
    P   O3P    gb_27
 [ exclusions ]
;  ai    aj
   CB   HD1
   CB   CE1
   CB   NE2
   CG     P
  ND1     P
  HD1   CD2
  HD1   NE2
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    CG     ga_14
   CB    CG   ND1     ga_36
   CB    CG   CD2     ga_36
  ND1    CG   CD2     ga_6
   CG   ND1   HD1     ga_35
   CG   ND1   CE1     ga_6
  HD1   ND1   CE1     ga_35
   CG   CD2   NE2     ga_6
  ND1   CE1   NE2     ga_6
  CD2   NE2   CE1     ga_6
  CD2   NE2     P     ga_33
  CE1   NE2     P     ga_33
  NE2     P   O1P     ga_4
  NE2     P   O2P     ga_4
  NE2     P   O3P     ga_4
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_13
  O2P     P   O3P     ga_13
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
   CG   ND1   CD2    CB     gi_1
  CD2    CG   ND1   CE1     gi_1
  ND1    CG   CD2   NE2     gi_1
   CG   ND1   CE1   NE2     gi_1
   CG   CD2   NE2   CE1     gi_1
  CD2   NE2   CE1   ND1     gi_1
  ND1    CG   CE1   HD1     gi_1
  NE2   CE1   CD2     P     gi_1
    P   O2P   O3P   O1P     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    CG     gd_17
   CA    CB    CG   ND1     gd_20
  CE1   NE2     P   O1P     gd_9

Regards,
Satyan

On Thu, 7 Feb 2008, Justin A. Lemkul wrote:

> Check the Users' Contributions site.  I believe there are some utilities for
> converting between AMBER and GROMACS formats.
>
> -Justin
>
> Quoting Eddie Mende <pckboy at gmail.com>:
>
> > Hello
> >
> > I just found a page with amber forcefield parameters for phosphohistidine
> > however these are to be used by the AMBER program
> > Is it easy (or is there any util) that I can use to translate parameters
> > form one
> > format into another?.
> >
> >
> > Eduardo
> > Justin A. Lemkul wrote:
> > > Eduardo,
> > >
> > > To my knowledge, no parameters exist for phosphorylated histidine.  You
> > will
> > > have to derive them in a manner consistent with the original forcefield.
> > If
> > > you are interested in breaking the His-PO3 bond, you will need to do some
> > > fairly rigorous QM/MM, for which an all-atom force field is the only way to
> > go
> > > (Amber or OPLSAA).  Sorry to say, I do not have parameters available for
> > either
> > > of these force fields that include your phosphorylated species.
> > >
> > > -Justin
> > _______________________________________________
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>
>
>
> ========================================
>
> 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/
>
> ========================================
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