Hi,
Have you checked the atom type present in the pdb file and the parameter
file for your phosphotyrosine residue? As I can see from the picture the
atoom types are OG, OP1, OP2, O3P which doesn't look consistent.
Soumya
On Mon, Dec 19, 2011 at 2:11 PM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Hi,
>
> I am simulating a protein which contains two phosphotyrosine residues using
> Amber 11 and ff99SB force field.
> For the parameters of Phosphotyrosine with single protonated phosphate
> group, i used the ones available at
> http://www.pharmacy.manchester.ac.uk/bryce/amber
> The structure obtained after 1000 cycles of minimization showed some
> connectivity problem in the phosphate group. An image showing the lack of
> connectivity between one of the phosphate oxygens is attached with this
> mail.
>
> The input I used for minimization is given below:
>
> complex: initial minimisation solvent + ions
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2500,
> ntpr = 25,
> cut = 10.0,
> /
>
> It will be very helpful if any one can tell me what is the reason for this
> problem. Any suggestions regarding this would be helpful.
>
>
> with regards,
>
> Sangeetha
> Research Scholar
> Centre for Bioinformatics
> Pondicherry University
> Pondicherry
>
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Received on Mon Dec 19 2011 - 01:30:02 PST
