On Sun, Sep 26, 2010, shweta wrote:
> a) In my protein two residues are phosphorylated, i generated parameters for
> phosphate group using Antechamber Module of AMBER , but when i upload the
> protein error message shows the missing parameters for these residues.
> Please suggest me how to generate parameters for these phosphorylated
> residues.
See the "contributed parameters database" at the Amber Web page.
> b) Also in these proteins two inbetween residues were missing, we tried to
> add it using modeller but in the resulting full protein these phosphate
> groups of two phosphorylated residues were missing, can we add these
> residues using AMBER so that the phosphorylated residues remain uneffected.
>
> These phosphorylated residues are important for MD simulation of protein
> under study. Kindly suggest me how to solve these problems.
Sounds like you will have to edit the two pdb files, manually inserting the
coordinates from the Modeller output into the one that has the
phosphorphylated residues (or vice versa).
....dac
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Received on Sun Sep 26 2010 - 07:00:03 PDT
