>
> My first goal is set up a good protocol to fit the protein:
>
> 1. Adjust hydrogens and protonation state
Hydrogens are added automatically when loading PDB in tleap program.
Optionally you could set protonation state of some histidines by
editing residue name HIS to HIE, HID or HIP in PDB.
> 2. Correct the lost aminoacides
You can use Swiss-PdbViewer program (that is free of charge) to add
missing residues to input PDB.
Another brief suggestions you can find on
http://enzyme.fbb.msu.ru/Tutorials/Tutorial_1/Sec_1.htm
and
http://enzyme.fbb.msu.ru/Tutorials/Tutorial_2/Sec_1.htm
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Apr 13 2011 - 02:00:03 PDT
