well in that case, can i use these commands for getting a good guess for
protonation states of whole system that have ligand.
reduce 4iae.pdb > 4iae_H.pdb
pdb4amber -i 4iae_H.pdb -o 4iae_H_renum.pdb
regards
On Mon, Sep 18, 2017 at 8:19 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 - 10:00:02 PDT
