[gmx-users] Treatment of protein termini when there are missing residues

[jo hanna]

Hello,

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.

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
to unknown artifacts. Another option would be to 'cap' or add a blocking
group
on the end of the protein chain, e.g. ACE, which introduces a group that
is non-native to this region of the protein. Or treat the end groups
neutrally. I have looked through the literature and while I can find
examples of MD being carried out with structures with missing residues at
the
termini, but I cannot find any description of how these groups are treated.

I would appreciate some views on this.

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
protein.

Many thanks,
Jo
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