Re: [AMBER] SEP non-standard phosphoserine issue.

From: Hai Nguyen <>
Date: Tue, 27 Dec 2016 02:22:21 -0500


seems like you can read previous post here:


On Tue, Dec 27, 2016 at 2:02 AM, Saman Yousuf ali <> wrote:

> Dear All,I am working on kinases. My protein target has some missing
> residues, I have added these missing gaps via modeller. Before modelling, I
> have converted two SEP (phosphoserine) non-standard aminoacid into SER
> because I got alignment error during modelling. After converting modified
> phosphoserine SEP into standard residue SER serine by just opening pdb text
> file and replace all SEP with SER, modeller added missing residue
> successfully. Now, I want to minimize this modelled protein to remove any
> steric clashes and bad contact by running MD simulation. I want to convert
> SER into SEP and to build library file for this nonstandard residue. Any
> suggestions would be greatly appreciated.Thank You Very Much Best,Saman
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Received on Mon Dec 26 2016 - 23:30:03 PST
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