On Sun, Sep 17, 2017, Rana Rehan Khalid wrote:
>
> If our protein's ligand have carboxylate-mediated interactions with the
> conserved YxSxR motif of protein as well as hydrophobic interactions,
> should we change the residues name like HIS to HID because it does not have
> bond with ligand. and CYS remain same according to our scenario.
By default, tleap treats HIS residues as HIE; edit the input pdb file if
you wish to change this to HID. (You can also set this in the leaprc file).
If CYS is not to be changed, then no editing of the pdb file is needed.
Generally, you want the input pdb file to reflect your choice of protonation
states. You can use the "--reduce" option in pdb4amber to get suggested
protonation states; these are often good suggestions, but are not always the
ones you wnat.
....dac
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Received on Mon Sep 18 2017 - 08:30:03 PDT
