[gmx-users] Phosphate bond angles in GDP

[Matthew Geballe]

Dear all,

I've been working for a couple weeks to build topologies for GTP and 
GDP in the G43a1 force field.  I did this by examining the ATP and GUA 
residues in the G43a1.rtp file.  However, in my trail runs with just 
GTP or GDP alone in a box of water there is a problem with the beta 
phosphate group on GDP.  The terminal oxygen atoms become planar with 
the the phosphorous atom.  However, I don't see this problem with the 
gamma phosphate of GTP even though as far as I can tell the gamma 
phosphate of GTP has the same paramaters as the beta phosphate of GDP.  
The .itp file are too large to include, but here are the relevant 
parameters for GTP and GDP.  If anyone could help me understand why 
this planarity occurs or catch the error in the files it would be 
greatly appreciated.

-Matt



GDP
(atoms)
      1 OM          1 GDP    O3B    0          -0.765    15.9994
      2 P           1 GDP    PB     0            0.63    30.9738
      3 OM          1 GDP    O2B    0          -0.765    15.9994
      4 OM          1 GDP    O1B    0          -0.765    15.9994
(bonds)
      2     1     2 gb_23     ;    PB   O3B
      2     3     2 gb_23     ;    PB   O2B
      2     4     2 gb_23     ;    PB   O1B
      2     5     2 gb_27     ;    PB   O3A
(pairs)
      2     7     1     ;    PB   O2A
      2     8     1     ;    PB   O1A
      2     9     1     ;    PB   O5*
      1     6     1     ;   O3B    PA
      3     6     1     ;   O2B    PA
      4     6     1     ;   O1B    PA
(angles)
      3     2     4     2  ga_28     ;   O2B    PB   O1B
      3     2     1     2  ga_28     ;   O2B    PB   O3B
      4     2     1     2  ga_28     ;   O1B    PB   O3B
      1     2     5     2  ga_13     ;   O3B    PB   O3A
      3     2     5     2  ga_13     ;   O2B    PB   O3A
      4     2     5     2  ga_13     ;   O1B    PB   O3A
      2     5     6     2  ga_25     ;    PB   O3A    PA
(dihedrals)
      2     1     4     3     2  gi_2     ;   IDI    PB   O3B   O1B   O2B
      3     2     5     6     1  gd_9     ;    DI   O2B    PB   O3A    PA
      3     2     5     6     1  gd_11    ;    DI   O2B    PB   O3A    PA
      2     5     6     9     1  gd_9     ;    DI    PB   O3A    PA   O5*
      2     5     6     9     1 gd_11     ;    DI    PB   O3A    PA   O5*


GTP

(atoms)
     1    OM     1   GTP     O2G     0   -0.770          15.9994
     2     P     1   GTP      PG     0    0.630          30.97380
     3    OM     1   GTP     O1G     0   -0.770          15.9994
     4    OM     1   GTP     O3G     0   -0.770          15.9994
(bonds)
     1   2   2   gb_23  ;           O2G   PG
     2   3   2   gb_23  ;            PG  O1G
     2   4   2   gb_23  ;            PG  O3G
     2   5   2   gb_27  ;            PG  O3B
(pairs)
1   6   1                   ;   O2G   PB
2   7   1                   ;    PG  O2B
2   8   1                   ;    PG  O1B
2   9   1                   ;    PG  O3A
3   6   1                   ;   O1G   PB
4   6   1                   ;   O3G   PB
(angles)
     1   2   3   2     ga_28    ;   O2G   PG  O1G
     1   2   4   2     ga_28    ;   O2G   PG  O3G
     3   2   4   2     ga_28    ;   O1G   PG  O3G
     1   2   5   2     ga_13    ;   O2G   PG  O3B
     3   2   5   2     ga_13    ;   O1G   PG  O3B
     4   2   5   2     ga_13    ;   O3G   PG  O3B
     2   5   6   2     ga_25    ;    PG  O3B   PB
(dihedrals)
     2   1   4   3   2     gi_2    ; IDI    PG  O2G  O3G  O1G
     6   5   2   1   1     gd_9    ; DI     PB  O3B   PG  O2G
     6   5   2   1   1     gd_11   ; DI     PB  O3B   PG  O2G
     2   5   6   9   1     gd_9    ; DI     PG  O3B   PB  O3A
     2   5   6   9   1     gd_11   ; DI     PG  O3B   PB  O3A