[gmx-users] phosphoserine

[David van der Spoel]

On Mon, 2002-09-02 at 10:55, emombel at nimr.mrc.ac.uk wrote:
> 
> 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?
No, just remove this interaction from the pairs list in the topology.
There also is a grompp option to do this IIRC
> 
> 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
> 
> 
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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