Dear Case,
Thank You for suggestion.
On Sun, Sep 26, 2010 at 7:19 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 - 22:00:03 PDT
