[AMBER] SEP non-standard phosphoserine issue.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Tue, 27 Dec 2016 07:02:47 +0000 (UTC)

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
AMBER mailing list
Received on Mon Dec 26 2016 - 23:30:03 PST
Custom Search