[gmx-users] phosphoserine

[emombel at nimr.mrc.ac.uk]

Dear All,
I have a phosporilated serine in my molecule, and I created the topology
file (attached if you are interested PSE residue).
Everything works fine except for the HO hydrogen attached to the P-OH.
It 'collapses' onto the  neighboring oxygen, considering that has no wand
der waals parameters and a negative charge, what else could he do?

If I remove this proton (PSO residue quite unrealistic because of the pKa
of ~12..)

everything works fine....

Do I have to add some restraints?

Any hints?

I used for the phosphoserine moiety the same parameters used for ATP.



[ PSE ]
 [ atoms ]
     N     N  -0.280     0
     H     H   0.280     0
    CA   CH1   0.000     1
    CB   CH2   0.150     2
    OP    OS  -0.360     2
    P1     P   0.630     2
   OM1    OM  -0.635     2
   OM2    OM  -0.635     2
   OMH    OA  -0.548     2
   HOP    HO   0.398     2
     C     C   0.380     3
     O     O  -0.380     3
 [ bonds ]
     N     H
     N    CA
    CA     C
     C     O
    -C     N
    CA    CB
    CB    OP
    OP    P1
    P1   OM1
    P1   OM2
    P1   OMH
    OMH  HOP
 [ impropers ]
     N    -C    CA     H
    -C   -CA     N    -O
    CA     N     C    CB

[ PSO ]
 [ atoms ]
     N     N  -0.280     0
     H     H   0.280     0
    CA   CH1   0.000     1
    CB   CH2   0.150     2
    OP    OS  -0.360     2
    P1     P   0.631     2
   OM1    OM  -0.807     2
   OM2    OM  -0.807     2
   OM3    OM  -0.807     2
     C     C   0.380     3
     O     O  -0.380     3
 [ bonds ]
     N     H
     N    CA
    CA     C
     C     O
    -C     N
    CA    CB
    CB    OP
    OP    P1
    P1   OM1
    P1   OM2
    P1   OM3
 [ impropers ]
     N    -C    CA     H
    -C   -CA     N    -O
    CA     N     C    CB
     P    OS    OM    OM


thanks
ff

Dr. Franca Fraternali
Mathematical Biology Division
National Institute for Medical Research
The Ridgeway, Mill Hill
NW7 1AA London
tel (direct) 02088162250
tel 0208 959 3666 ext. 2250
fax 0208 906 4477 /02088162460
http://mathbio.nimr.mrc.ac.uk