Hello,<br><br>My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb.<br>
<br>
My thoughts are that assigning charges to the end groups will result in areas of charge in regions where there may not be any in the native protein and could lead<br>
to unknown artifacts. Another option would be to 'cap' or add a blocking group<br>
on the end of the protein chain, e.g. ACE, which introduces a group that<br>
is non-native to this region of the protein. Or treat the end groups<br>
neutrally. I have looked through the literature and while I can find<br>
examples of MD being carried out with structures with missing residues at the<br>
termini, but I cannot find any description of how these groups are treated.<br><br>I would appreciate some views on this. <br><br>N.B. The protein I am wishing to study is catalytically active and therefore I have confidence that these missing residues have no effect on the activity of the<br>
protein.<br><br>Many thanks,<br>Jo<br><br>